diff --git a/control_plane/src/pageserver.rs b/control_plane/src/pageserver.rs
index 5a84763697697..a8fa8486e8c52 100644
--- a/control_plane/src/pageserver.rs
+++ b/control_plane/src/pageserver.rs
@@ -17,7 +17,7 @@ use anyhow::{bail, Context};
 use camino::Utf8PathBuf;
 use futures::SinkExt;
 use pageserver_api::models::{
-    self, AuxFilePolicy, LocationConfig, ShardParameters, TenantHistorySize, TenantInfo,
+    self, LocationConfig, ShardParameters, SwitchAuxFilePolicy, TenantHistorySize, TenantInfo,
     TimelineInfo,
 };
 use pageserver_api::shard::TenantShardId;
@@ -380,7 +380,7 @@ impl PageServerNode {
                 .context("parse `timeline_get_throttle` from json")?,
             switch_aux_file_policy: settings
                 .remove("switch_aux_file_policy")
-                .map(|x| x.parse::<AuxFilePolicy>())
+                .map(|x| x.parse::<SwitchAuxFilePolicy>())
                 .transpose()
                 .context("Failed to parse 'switch_aux_file_policy'")?,
         };
@@ -503,7 +503,7 @@ impl PageServerNode {
                     .context("parse `timeline_get_throttle` from json")?,
                 switch_aux_file_policy: settings
                     .remove("switch_aux_file_policy")
-                    .map(|x| x.parse::<AuxFilePolicy>())
+                    .map(|x| x.parse::<SwitchAuxFilePolicy>())
                     .transpose()
                     .context("Failed to parse 'switch_aux_file_policy'")?,
             }
diff --git a/libs/pageserver_api/src/models.rs b/libs/pageserver_api/src/models.rs
index 1df5820fb946d..8e68a7c3ba078 100644
--- a/libs/pageserver_api/src/models.rs
+++ b/libs/pageserver_api/src/models.rs
@@ -10,6 +10,7 @@ use std::{
     io::{BufRead, Read},
     num::{NonZeroU64, NonZeroUsize},
     str::FromStr,
+    sync::atomic::AtomicUsize,
     time::{Duration, SystemTime},
 };
 
@@ -305,17 +306,107 @@ pub struct TenantConfig {
     pub lazy_slru_download: Option<bool>,
     pub timeline_get_throttle: Option<ThrottleConfig>,
     pub image_layer_creation_check_threshold: Option<u8>,
-    pub switch_aux_file_policy: Option<AuxFilePolicy>,
+    pub switch_aux_file_policy: Option<SwitchAuxFilePolicy>,
 }
 
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
-pub enum AuxFilePolicy {
+pub enum SwitchAuxFilePolicy {
     V1,
     V2,
     CrossValidation,
 }
 
-impl FromStr for AuxFilePolicy {
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
+pub enum RuntimeAuxFilePolicy {
+    V1,
+    V2,
+    CrossValidation,
+    Unspecified,
+}
+
+pub struct AtomicRuntimeAuxFilePolicy(AtomicUsize);
+
+impl AtomicRuntimeAuxFilePolicy {
+    pub fn new(policy: RuntimeAuxFilePolicy) -> Self {
+        Self(AtomicUsize::new(policy.to_usize()))
+    }
+
+    pub fn load(&self) -> RuntimeAuxFilePolicy {
+        RuntimeAuxFilePolicy::from_usize(self.0.load(std::sync::atomic::Ordering::SeqCst))
+    }
+
+    pub fn store(&self, policy: RuntimeAuxFilePolicy) {
+        self.0.store(
+            RuntimeAuxFilePolicy::to_usize(policy),
+            std::sync::atomic::Ordering::SeqCst,
+        );
+    }
+}
+
+impl SwitchAuxFilePolicy {
+    pub fn to_usize(self) -> usize {
+        match self {
+            Self::V1 => 1,
+            Self::CrossValidation => 2,
+            Self::V2 => 3,
+        }
+    }
+
+    pub fn from_usize(this: usize) -> Self {
+        match this {
+            1 => Self::V1,
+            2 => Self::CrossValidation,
+            3 => Self::V2,
+            _ => unreachable!(),
+        }
+    }
+
+    pub fn to_runtime_policy(&self) -> RuntimeAuxFilePolicy {
+        RuntimeAuxFilePolicy::from_usize(self.to_usize())
+    }
+}
+
+impl RuntimeAuxFilePolicy {
+    pub fn to_usize(self) -> usize {
+        match self {
+            Self::V1 => 1,
+            Self::CrossValidation => 2,
+            Self::V2 => 3,
+            Self::Unspecified => 0,
+        }
+    }
+
+    pub fn from_usize(this: usize) -> Self {
+        match this {
+            1 => Self::V1,
+            2 => Self::CrossValidation,
+            3 => Self::V2,
+            0 => Self::Unspecified,
+            _ => unreachable!(),
+        }
+    }
+}
+
+impl FromStr for RuntimeAuxFilePolicy {
+    type Err = anyhow::Error;
+
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        let s = s.to_lowercase();
+        if s == "" || s == "unspecified" {
+            return Ok(Self::Unspecified);
+        } else if s == "v1" {
+            Ok(Self::V1)
+        } else if s == "v2" {
+            Ok(Self::V2)
+        } else if s == "crossvalidation" || s == "cross_validation" {
+            Ok(Self::CrossValidation)
+        } else {
+            anyhow::bail!("cannot parse {} to aux file policy", s)
+        }
+    }
+}
+
+impl FromStr for SwitchAuxFilePolicy {
     type Err = anyhow::Error;
 
     fn from_str(s: &str) -> Result<Self, Self::Err> {
@@ -604,6 +695,9 @@ pub struct TimelineInfo {
     pub state: TimelineState,
 
     pub walreceiver_status: String,
+
+    /// Whether aux file v2 is enabled
+    pub last_aux_file_policy: RuntimeAuxFilePolicy,
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize)]
diff --git a/pageserver/ctl/src/main.rs b/pageserver/ctl/src/main.rs
index 1fb75584fc921..e92c352dab1d5 100644
--- a/pageserver/ctl/src/main.rs
+++ b/pageserver/ctl/src/main.rs
@@ -219,6 +219,7 @@ fn handle_metadata(
     let mut meta = TimelineMetadata::from_bytes(&metadata_bytes)?;
     println!("Current metadata:\n{meta:?}");
     let mut update_meta = false;
+    // TODO: simplify this part
     if let Some(disk_consistent_lsn) = disk_consistent_lsn {
         meta = TimelineMetadata::new(
             *disk_consistent_lsn,
diff --git a/pageserver/src/http/routes.rs b/pageserver/src/http/routes.rs
index a8ca642dc59af..8fcf84f5d1dee 100644
--- a/pageserver/src/http/routes.rs
+++ b/pageserver/src/http/routes.rs
@@ -433,6 +433,8 @@ async fn build_timeline_info_common(
         state,
 
         walreceiver_status,
+
+        last_aux_file_policy: timeline.last_aux_file_policy.load(),
     };
     Ok(info)
 }
diff --git a/pageserver/src/pgdatadir_mapping.rs b/pageserver/src/pgdatadir_mapping.rs
index a4215ee107b2f..1ddd089e1bbd0 100644
--- a/pageserver/src/pgdatadir_mapping.rs
+++ b/pageserver/src/pgdatadir_mapping.rs
@@ -24,7 +24,7 @@ use pageserver_api::key::{
     AUX_FILES_KEY, CHECKPOINT_KEY, CONTROLFILE_KEY, DBDIR_KEY, TWOPHASEDIR_KEY,
 };
 use pageserver_api::keyspace::SparseKeySpace;
-use pageserver_api::models::AuxFilePolicy;
+use pageserver_api::models::{RuntimeAuxFilePolicy, SwitchAuxFilePolicy};
 use pageserver_api::reltag::{BlockNumber, RelTag, SlruKind};
 use postgres_ffi::relfile_utils::{FSM_FORKNUM, VISIBILITYMAP_FORKNUM};
 use postgres_ffi::BLCKSZ;
@@ -35,7 +35,7 @@ use std::ops::ControlFlow;
 use std::ops::Range;
 use strum::IntoEnumIterator;
 use tokio_util::sync::CancellationToken;
-use tracing::{debug, trace, warn};
+use tracing::{debug, info, trace, warn};
 use utils::bin_ser::DeserializeError;
 use utils::vec_map::{VecMap, VecMapOrdering};
 use utils::{bin_ser::BeSer, lsn::Lsn};
@@ -714,10 +714,13 @@ impl Timeline {
         lsn: Lsn,
         ctx: &RequestContext,
     ) -> Result<HashMap<String, Bytes>, PageReconstructError> {
-        match self.get_switch_aux_file_policy() {
-            AuxFilePolicy::V1 => self.list_aux_files_v1(lsn, ctx).await,
-            AuxFilePolicy::V2 => self.list_aux_files_v2(lsn, ctx).await,
-            AuxFilePolicy::CrossValidation => {
+        let current_policy = self.last_aux_file_policy.load();
+        match current_policy {
+            RuntimeAuxFilePolicy::V1 | RuntimeAuxFilePolicy::Unspecified => {
+                self.list_aux_files_v1(lsn, ctx).await
+            }
+            RuntimeAuxFilePolicy::V2 => self.list_aux_files_v2(lsn, ctx).await,
+            RuntimeAuxFilePolicy::CrossValidation => {
                 let v1_result = self.list_aux_files_v1(lsn, ctx).await;
                 let v2_result = self.list_aux_files_v2(lsn, ctx).await;
                 match (v1_result, v2_result) {
@@ -1447,7 +1450,7 @@ impl<'a> DatadirModification<'a> {
     }
 
     pub fn init_aux_dir(&mut self) -> anyhow::Result<()> {
-        if let AuxFilePolicy::V2 = self.tline.get_switch_aux_file_policy() {
+        if let SwitchAuxFilePolicy::V2 = self.tline.get_switch_aux_file_policy() {
             return Ok(());
         }
         let buf = AuxFilesDirectory::ser(&AuxFilesDirectory {
@@ -1465,8 +1468,34 @@ impl<'a> DatadirModification<'a> {
         content: &[u8],
         ctx: &RequestContext,
     ) -> anyhow::Result<()> {
-        let policy = self.tline.get_switch_aux_file_policy();
-        if let AuxFilePolicy::V2 | AuxFilePolicy::CrossValidation = policy {
+        let switch_policy = self.tline.get_switch_aux_file_policy();
+
+        let policy = {
+            let current_policy = self.tline.last_aux_file_policy.load();
+            // Allowed switch path:
+            // * no aux files -> v1/v2/cross-validation
+            // * cross-validation->v2
+            match (current_policy, switch_policy) {
+                (RuntimeAuxFilePolicy::Unspecified, _)
+                | (RuntimeAuxFilePolicy::CrossValidation, SwitchAuxFilePolicy::V2) => {
+                    let new_policy = switch_policy.to_runtime_policy();
+                    self.tline.last_aux_file_policy.store(new_policy);
+                    info!("switching to aux file policy {:?}", new_policy);
+                    if let Some(ref remote_client) = self.tline.remote_client {
+                        remote_client
+                            .schedule_index_upload_for_aux_file_policy_update(new_policy)?;
+                        remote_client.wait_completion().await?;
+                    }
+                    info!("finish switching to aux file policy {:?}", new_policy);
+                    new_policy
+                }
+                (current_policy, _) => current_policy,
+            }
+        };
+
+        assert!(policy != RuntimeAuxFilePolicy::Unspecified);
+
+        if let RuntimeAuxFilePolicy::V2 | RuntimeAuxFilePolicy::CrossValidation = policy {
             let key = aux_file::encode_aux_file_key(path);
             // retrieve the key from the engine
             let old_val = match self.get(key, ctx).await {
@@ -1495,7 +1524,7 @@ impl<'a> DatadirModification<'a> {
             self.put(key, Value::Image(new_val.into()));
         }
 
-        if let AuxFilePolicy::V1 | AuxFilePolicy::CrossValidation = policy {
+        if let RuntimeAuxFilePolicy::V1 | RuntimeAuxFilePolicy::CrossValidation = policy {
             let file_path = path.to_string();
             let content = if content.is_empty() {
                 None
diff --git a/pageserver/src/tenant.rs b/pageserver/src/tenant.rs
index 010e56a899db4..bfe8ea57688bf 100644
--- a/pageserver/src/tenant.rs
+++ b/pageserver/src/tenant.rs
@@ -20,6 +20,7 @@ use futures::stream::FuturesUnordered;
 use futures::FutureExt;
 use futures::StreamExt;
 use pageserver_api::models;
+use pageserver_api::models::RuntimeAuxFilePolicy;
 use pageserver_api::models::TimelineState;
 use pageserver_api::models::WalRedoManagerStatus;
 use pageserver_api::shard::ShardIdentity;
@@ -528,6 +529,7 @@ impl Tenant {
         index_part: Option<IndexPart>,
         metadata: TimelineMetadata,
         ancestor: Option<Arc<Timeline>>,
+        last_aux_file_policy: RuntimeAuxFilePolicy,
         _ctx: &RequestContext,
     ) -> anyhow::Result<()> {
         let tenant_id = self.tenant_shard_id;
@@ -538,6 +540,10 @@ impl Tenant {
             ancestor.clone(),
             resources,
             CreateTimelineCause::Load,
+            // This could be derived from ancestor branch + index part. Though the only caller of `timeline_init_and_sync` is `load_remote_timeline`,
+            // there will potentially be other caller of this function in the future, and we don't know whether `index_part` or `ancestor` takes precedence.
+            // Therefore, we pass this field explicitly for now, and remove it once we fully migrate to aux file v2.
+            last_aux_file_policy,
         )?;
         let disk_consistent_lsn = timeline.get_disk_consistent_lsn();
         anyhow::ensure!(
@@ -1176,12 +1182,15 @@ impl Tenant {
             None
         };
 
+        let last_aux_file_policy = index_part.last_aux_file_policy();
+
         self.timeline_init_and_sync(
             timeline_id,
             resources,
             Some(index_part),
             remote_metadata,
             ancestor,
+            last_aux_file_policy,
             ctx,
         )
         .await
@@ -1360,6 +1369,7 @@ impl Tenant {
             create_guard,
             initdb_lsn,
             None,
+            RuntimeAuxFilePolicy::Unspecified,
         )
         .await
     }
@@ -2431,6 +2441,7 @@ impl Tenant {
         ancestor: Option<Arc<Timeline>>,
         resources: TimelineResources,
         cause: CreateTimelineCause,
+        last_aux_file_policy: RuntimeAuxFilePolicy,
     ) -> anyhow::Result<Arc<Timeline>> {
         let state = match cause {
             CreateTimelineCause::Load => {
@@ -2459,6 +2470,7 @@ impl Tenant {
             resources,
             pg_version,
             state,
+            last_aux_file_policy,
             self.cancel.child_token(),
         );
 
@@ -3109,6 +3121,7 @@ impl Tenant {
                 timeline_create_guard,
                 start_lsn + 1,
                 Some(Arc::clone(src_timeline)),
+                src_timeline.last_aux_file_policy.load(),
             )
             .await?;
 
@@ -3311,6 +3324,7 @@ impl Tenant {
                 timeline_create_guard,
                 pgdata_lsn,
                 None,
+                RuntimeAuxFilePolicy::Unspecified,
             )
             .await?;
 
@@ -3388,6 +3402,7 @@ impl Tenant {
         create_guard: TimelineCreateGuard<'a>,
         start_lsn: Lsn,
         ancestor: Option<Arc<Timeline>>,
+        last_aux_file_policy: RuntimeAuxFilePolicy,
     ) -> anyhow::Result<UninitializedTimeline> {
         let tenant_shard_id = self.tenant_shard_id;
 
@@ -3403,6 +3418,7 @@ impl Tenant {
                 ancestor,
                 resources,
                 CreateTimelineCause::Load,
+                last_aux_file_policy,
             )
             .context("Failed to create timeline data structure")?;
 
diff --git a/pageserver/src/tenant/config.rs b/pageserver/src/tenant/config.rs
index a743ce3c16a30..b5a46713d98a3 100644
--- a/pageserver/src/tenant/config.rs
+++ b/pageserver/src/tenant/config.rs
@@ -9,9 +9,9 @@
 //! may lead to a data loss.
 //!
 use anyhow::bail;
-use pageserver_api::models::AuxFilePolicy;
 use pageserver_api::models::CompactionAlgorithm;
 use pageserver_api::models::EvictionPolicy;
+use pageserver_api::models::SwitchAuxFilePolicy;
 use pageserver_api::models::{self, ThrottleConfig};
 use pageserver_api::shard::{ShardCount, ShardIdentity, ShardNumber, ShardStripeSize};
 use serde::de::IntoDeserializer;
@@ -373,7 +373,7 @@ pub struct TenantConf {
 
     /// Switch to a new aux file policy. Switching this flag requires the user has not written any aux file into
     /// the storage before, and this flag cannot be switched back. Otherwise there will be data corruptions.
-    pub switch_aux_file_policy: AuxFilePolicy,
+    pub switch_aux_file_policy: SwitchAuxFilePolicy,
 }
 
 /// Same as TenantConf, but this struct preserves the information about
@@ -472,7 +472,7 @@ pub struct TenantConfOpt {
 
     #[serde(skip_serializing_if = "Option::is_none")]
     #[serde(default)]
-    pub switch_aux_file_policy: Option<AuxFilePolicy>,
+    pub switch_aux_file_policy: Option<SwitchAuxFilePolicy>,
 }
 
 impl TenantConfOpt {
@@ -574,7 +574,7 @@ impl Default for TenantConf {
             lazy_slru_download: false,
             timeline_get_throttle: crate::tenant::throttle::Config::disabled(),
             image_layer_creation_check_threshold: DEFAULT_IMAGE_LAYER_CREATION_CHECK_THRESHOLD,
-            switch_aux_file_policy: AuxFilePolicy::V1,
+            switch_aux_file_policy: SwitchAuxFilePolicy::V1,
         }
     }
 }
diff --git a/pageserver/src/tenant/remote_timeline_client.rs b/pageserver/src/tenant/remote_timeline_client.rs
index bbe4e16378a15..62e46ad4247bb 100644
--- a/pageserver/src/tenant/remote_timeline_client.rs
+++ b/pageserver/src/tenant/remote_timeline_client.rs
@@ -189,6 +189,7 @@ use camino::Utf8Path;
 use chrono::{NaiveDateTime, Utc};
 
 pub(crate) use download::download_initdb_tar_zst;
+use pageserver_api::models::RuntimeAuxFilePolicy;
 use pageserver_api::shard::{ShardIndex, TenantShardId};
 use scopeguard::ScopeGuard;
 use tokio_util::sync::CancellationToken;
@@ -596,6 +597,17 @@ impl RemoteTimelineClient {
         Ok(())
     }
 
+    /// Launch an index-file upload operation in the background, with only aux_file_policy flag updated.
+    pub(crate) fn schedule_index_upload_for_aux_file_policy_update(
+        self: &Arc<Self>,
+        last_aux_file_policy: RuntimeAuxFilePolicy,
+    ) -> anyhow::Result<()> {
+        let mut guard = self.upload_queue.lock().unwrap();
+        let upload_queue = guard.initialized_mut()?;
+        upload_queue.last_aux_file_policy = last_aux_file_policy;
+        self.schedule_index_upload(upload_queue);
+        Ok(())
+    }
     ///
     /// Launch an index-file upload operation in the background, if necessary.
     ///
@@ -923,7 +935,7 @@ impl RemoteTimelineClient {
     }
 
     /// Wait for all previously scheduled uploads/deletions to complete
-    pub(crate) async fn wait_completion(self: &Arc<Self>) -> anyhow::Result<()> {
+    pub async fn wait_completion(self: &Arc<Self>) -> anyhow::Result<()> {
         let receiver = {
             let mut guard = self.upload_queue.lock().unwrap();
             let upload_queue = guard.initialized_mut()?;
@@ -1824,6 +1836,7 @@ impl RemoteTimelineClient {
                         dangling_files: HashMap::default(),
                         shutting_down: false,
                         shutdown_ready: Arc::new(tokio::sync::Semaphore::new(0)),
+                        last_aux_file_policy: initialized.last_aux_file_policy,
                     };
 
                     let upload_queue = std::mem::replace(
diff --git a/pageserver/src/tenant/remote_timeline_client/index.rs b/pageserver/src/tenant/remote_timeline_client/index.rs
index 3e05905afafb0..19941971ddeb7 100644
--- a/pageserver/src/tenant/remote_timeline_client/index.rs
+++ b/pageserver/src/tenant/remote_timeline_client/index.rs
@@ -5,6 +5,7 @@
 use std::collections::HashMap;
 
 use chrono::NaiveDateTime;
+use pageserver_api::models::RuntimeAuxFilePolicy;
 use serde::{Deserialize, Serialize};
 
 use crate::tenant::metadata::TimelineMetadata;
@@ -84,6 +85,9 @@ pub struct IndexPart {
 
     #[serde(rename = "metadata_bytes")]
     pub metadata: TimelineMetadata,
+
+    // Added in version 5. None == RuntimeAuxFilePolicy::Unspecified. Use Option wrapper to keep forward compatibility.
+    pub last_aux_file_policy: Option<RuntimeAuxFilePolicy>,
 }
 
 impl IndexPart {
@@ -96,10 +100,11 @@ impl IndexPart {
     /// - 3: no longer deserialize `timeline_layers` (serialized format is the same, but timeline_layers
     ///      is always generated from the keys of `layer_metadata`)
     /// - 4: timeline_layers is fully removed.
-    const LATEST_VERSION: usize = 4;
+    /// - 5: last_aux_file_policy is added.
+    const LATEST_VERSION: usize = 5;
 
     // Versions we may see when reading from a bucket.
-    pub const KNOWN_VERSIONS: &'static [usize] = &[1, 2, 3, 4];
+    pub const KNOWN_VERSIONS: &'static [usize] = &[1, 2, 3, 4, 5];
 
     pub const FILE_NAME: &'static str = "index_part.json";
 
@@ -107,6 +112,7 @@ impl IndexPart {
         layers_and_metadata: &HashMap<LayerName, LayerFileMetadata>,
         disk_consistent_lsn: Lsn,
         metadata: TimelineMetadata,
+        last_aux_file_policy: RuntimeAuxFilePolicy,
     ) -> Self {
         let layer_metadata = layers_and_metadata
             .iter()
@@ -119,6 +125,7 @@ impl IndexPart {
             disk_consistent_lsn,
             metadata,
             deleted_at: None,
+            last_aux_file_policy: Some(last_aux_file_policy),
         }
     }
 
@@ -147,8 +154,14 @@ impl IndexPart {
             &HashMap::new(),
             example_metadata.disk_consistent_lsn(),
             example_metadata,
+            RuntimeAuxFilePolicy::V2,
         )
     }
+
+    pub fn last_aux_file_policy(&self) -> RuntimeAuxFilePolicy {
+        self.last_aux_file_policy
+            .unwrap_or(RuntimeAuxFilePolicy::Unspecified)
+    }
 }
 
 impl From<&UploadQueueInitialized> for IndexPart {
@@ -156,7 +169,12 @@ impl From<&UploadQueueInitialized> for IndexPart {
         let disk_consistent_lsn = uq.latest_metadata.disk_consistent_lsn();
         let metadata = uq.latest_metadata.clone();
 
-        Self::new(&uq.latest_files, disk_consistent_lsn, metadata)
+        Self::new(
+            &uq.latest_files,
+            disk_consistent_lsn,
+            metadata,
+            uq.last_aux_file_policy,
+        )
     }
 }
 
@@ -221,6 +239,7 @@ mod tests {
             disk_consistent_lsn: "0/16960E8".parse::<Lsn>().unwrap(),
             metadata: TimelineMetadata::from_bytes(&[113,11,159,210,0,54,0,4,0,0,0,0,1,105,96,232,1,0,0,0,0,1,105,96,112,0,0,0,0,0,0,0,0,0,0,0,0,0,1,105,96,112,0,0,0,0,1,105,96,112,0,0,0,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]).unwrap(),
             deleted_at: None,
+            last_aux_file_policy: None,
         };
 
         let part = IndexPart::from_s3_bytes(example.as_bytes()).unwrap();
@@ -261,6 +280,7 @@ mod tests {
             disk_consistent_lsn: "0/16960E8".parse::<Lsn>().unwrap(),
             metadata: TimelineMetadata::from_bytes(&[113,11,159,210,0,54,0,4,0,0,0,0,1,105,96,232,1,0,0,0,0,1,105,96,112,0,0,0,0,0,0,0,0,0,0,0,0,0,1,105,96,112,0,0,0,0,1,105,96,112,0,0,0,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]).unwrap(),
             deleted_at: None,
+            last_aux_file_policy: None,
         };
 
         let part = IndexPart::from_s3_bytes(example.as_bytes()).unwrap();
@@ -302,7 +322,8 @@ mod tests {
             disk_consistent_lsn: "0/16960E8".parse::<Lsn>().unwrap(),
             metadata: TimelineMetadata::from_bytes(&[113,11,159,210,0,54,0,4,0,0,0,0,1,105,96,232,1,0,0,0,0,1,105,96,112,0,0,0,0,0,0,0,0,0,0,0,0,0,1,105,96,112,0,0,0,0,1,105,96,112,0,0,0,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]).unwrap(),
             deleted_at: Some(chrono::NaiveDateTime::parse_from_str(
-                "2023-07-31T09:00:00.123000000", "%Y-%m-%dT%H:%M:%S.%f").unwrap())
+                "2023-07-31T09:00:00.123000000", "%Y-%m-%dT%H:%M:%S.%f").unwrap()),
+                last_aux_file_policy: None,
         };
 
         let part = IndexPart::from_s3_bytes(example.as_bytes()).unwrap();
@@ -347,6 +368,7 @@ mod tests {
             ])
             .unwrap(),
             deleted_at: None,
+            last_aux_file_policy: None,
         };
 
         let empty_layers_parsed = IndexPart::from_s3_bytes(empty_layers_json.as_bytes()).unwrap();
@@ -387,6 +409,48 @@ mod tests {
             metadata: TimelineMetadata::from_bytes(&[113,11,159,210,0,54,0,4,0,0,0,0,1,105,96,232,1,0,0,0,0,1,105,96,112,0,0,0,0,0,0,0,0,0,0,0,0,0,1,105,96,112,0,0,0,0,1,105,96,112,0,0,0,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]).unwrap(),
             deleted_at: Some(chrono::NaiveDateTime::parse_from_str(
                 "2023-07-31T09:00:00.123000000", "%Y-%m-%dT%H:%M:%S.%f").unwrap()),
+                last_aux_file_policy: None,
+        };
+
+        let part = IndexPart::from_s3_bytes(example.as_bytes()).unwrap();
+        assert_eq!(part, expected);
+    }
+
+    #[test]
+    fn v5_indexpart_is_parsed() {
+        let example = r#"{
+            "version":5,
+            "layer_metadata":{
+                "000000000000000000000000000000000000-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF__0000000001696070-00000000016960E9": { "file_size": 25600000 },
+                "000000000000000000000000000000000000-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF__00000000016B59D8-00000000016B5A51": { "file_size": 9007199254741001 }
+            },
+            "disk_consistent_lsn":"0/16960E8",
+            "metadata_bytes":[113,11,159,210,0,54,0,4,0,0,0,0,1,105,96,232,1,0,0,0,0,1,105,96,112,0,0,0,0,0,0,0,0,0,0,0,0,0,1,105,96,112,0,0,0,0,1,105,96,112,0,0,0,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
+            "deleted_at": "2023-07-31T09:00:00.123",
+            "last_aux_file_policy": "V2"
+        }"#;
+
+        let expected = IndexPart {
+            version: 5,
+            layer_metadata: HashMap::from([
+                ("000000000000000000000000000000000000-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF__0000000001696070-00000000016960E9".parse().unwrap(), IndexLayerMetadata {
+                    file_size: 25600000,
+                    generation: Generation::none(),
+                    shard: ShardIndex::unsharded()
+                }),
+                ("000000000000000000000000000000000000-FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF__00000000016B59D8-00000000016B5A51".parse().unwrap(), IndexLayerMetadata {
+                    // serde_json should always parse this but this might be a double with jq for
+                    // example.
+                    file_size: 9007199254741001,
+                    generation: Generation::none(),
+                    shard: ShardIndex::unsharded()
+                })
+            ]),
+            disk_consistent_lsn: "0/16960E8".parse::<Lsn>().unwrap(),
+            metadata: TimelineMetadata::from_bytes(&[113,11,159,210,0,54,0,4,0,0,0,0,1,105,96,232,1,0,0,0,0,1,105,96,112,0,0,0,0,0,0,0,0,0,0,0,0,0,1,105,96,112,0,0,0,0,1,105,96,112,0,0,0,14,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]).unwrap(),
+            deleted_at: Some(chrono::NaiveDateTime::parse_from_str(
+                "2023-07-31T09:00:00.123000000", "%Y-%m-%dT%H:%M:%S.%f").unwrap()),
+            last_aux_file_policy:Some(RuntimeAuxFilePolicy::V2),
         };
 
         let part = IndexPart::from_s3_bytes(example.as_bytes()).unwrap();
diff --git a/pageserver/src/tenant/timeline.rs b/pageserver/src/tenant/timeline.rs
index 7edb922069c0a..7e89bebc4de5c 100644
--- a/pageserver/src/tenant/timeline.rs
+++ b/pageserver/src/tenant/timeline.rs
@@ -23,9 +23,9 @@ use pageserver_api::{
     },
     keyspace::{KeySpaceAccum, SparseKeyPartitioning},
     models::{
-        AuxFilePolicy, CompactionAlgorithm, DownloadRemoteLayersTaskInfo,
+        AtomicRuntimeAuxFilePolicy, CompactionAlgorithm, DownloadRemoteLayersTaskInfo,
         DownloadRemoteLayersTaskSpawnRequest, EvictionPolicy, InMemoryLayerInfo, LayerMapInfo,
-        TimelineState,
+        RuntimeAuxFilePolicy, SwitchAuxFilePolicy, TimelineState,
     },
     reltag::BlockNumber,
     shard::{ShardIdentity, ShardNumber, TenantShardId},
@@ -409,6 +409,9 @@ pub struct Timeline {
 
     /// Keep aux directory cache to avoid it's reconstruction on each update
     pub(crate) aux_files: tokio::sync::Mutex<AuxFilesState>,
+
+    /// Indicate whether aux file v2 storage is enabled.
+    pub(crate) last_aux_file_policy: AtomicRuntimeAuxFilePolicy,
 }
 
 pub struct WalReceiverInfo {
@@ -2000,7 +2003,7 @@ const REPARTITION_FREQ_IN_CHECKPOINT_DISTANCE: u64 = 10;
 
 // Private functions
 impl Timeline {
-    pub(crate) fn get_switch_aux_file_policy(&self) -> AuxFilePolicy {
+    pub(crate) fn get_switch_aux_file_policy(&self) -> SwitchAuxFilePolicy {
         let tenant_conf = self.tenant_conf.load();
         tenant_conf
             .tenant_conf
@@ -2138,6 +2141,7 @@ impl Timeline {
         resources: TimelineResources,
         pg_version: u32,
         state: TimelineState,
+        aux_file_policy: RuntimeAuxFilePolicy,
         cancel: CancellationToken,
     ) -> Arc<Self> {
         let disk_consistent_lsn = metadata.disk_consistent_lsn();
@@ -2257,6 +2261,8 @@ impl Timeline {
                     dir: None,
                     n_deltas: 0,
                 }),
+
+                last_aux_file_policy: AtomicRuntimeAuxFilePolicy::new(aux_file_policy),
             };
             result.repartition_threshold =
                 result.get_checkpoint_distance() / REPARTITION_FREQ_IN_CHECKPOINT_DISTANCE;
@@ -2406,6 +2412,11 @@ impl Timeline {
         let shard = self.get_shard_index();
         let this = self.myself.upgrade().expect("&self method holds the arc");
 
+        if let Some(ref index_part) = index_part {
+            self.last_aux_file_policy
+                .store(index_part.last_aux_file_policy());
+        }
+
         let (loaded_layers, needs_cleanup, total_physical_size) = tokio::task::spawn_blocking({
             move || {
                 let _g = span.entered();
diff --git a/pageserver/src/tenant/timeline/delete.rs b/pageserver/src/tenant/timeline/delete.rs
index d8701be170132..471a1e50310b0 100644
--- a/pageserver/src/tenant/timeline/delete.rs
+++ b/pageserver/src/tenant/timeline/delete.rs
@@ -4,7 +4,10 @@ use std::{
 };
 
 use anyhow::Context;
-use pageserver_api::{models::TimelineState, shard::TenantShardId};
+use pageserver_api::{
+    models::{RuntimeAuxFilePolicy, TimelineState},
+    shard::TenantShardId,
+};
 use tokio::sync::OwnedMutexGuard;
 use tracing::{error, info, instrument, Instrument};
 use utils::{crashsafe, fs_ext, id::TimelineId};
@@ -278,6 +281,7 @@ impl DeleteTimelineFlow {
                 // Important. We dont pass ancestor above because it can be missing.
                 // Thus we need to skip the validation here.
                 CreateTimelineCause::Delete,
+                RuntimeAuxFilePolicy::Unspecified, // Aux file policy is not needed for deletion, assuming deletion does not read aux keyspace
             )
             .context("create_timeline_struct")?;
 
diff --git a/pageserver/src/tenant/upload_queue.rs b/pageserver/src/tenant/upload_queue.rs
index 7797117e0f0f6..6bce47c285be7 100644
--- a/pageserver/src/tenant/upload_queue.rs
+++ b/pageserver/src/tenant/upload_queue.rs
@@ -7,6 +7,7 @@ use std::collections::{HashMap, VecDeque};
 use std::fmt::Debug;
 
 use chrono::NaiveDateTime;
+use pageserver_api::models::RuntimeAuxFilePolicy;
 use std::sync::Arc;
 use tracing::info;
 use utils::lsn::AtomicLsn;
@@ -56,6 +57,8 @@ pub(crate) struct UploadQueueInitialized {
     /// DANGER: do not return to outside world, e.g., safekeepers.
     pub(crate) latest_metadata: TimelineMetadata,
 
+    pub(crate) last_aux_file_policy: RuntimeAuxFilePolicy,
+
     /// `disk_consistent_lsn` from the last metadata file that was successfully
     /// uploaded. `Lsn(0)` if nothing was uploaded yet.
     /// Unlike `latest_files` or `latest_metadata`, this value is never ahead.
@@ -184,6 +187,7 @@ impl UploadQueue {
             dangling_files: HashMap::new(),
             shutting_down: false,
             shutdown_ready: Arc::new(tokio::sync::Semaphore::new(0)),
+            last_aux_file_policy: RuntimeAuxFilePolicy::Unspecified,
         };
 
         *self = UploadQueue::Initialized(state);
@@ -233,6 +237,7 @@ impl UploadQueue {
             dangling_files: HashMap::new(),
             shutting_down: false,
             shutdown_ready: Arc::new(tokio::sync::Semaphore::new(0)),
+            last_aux_file_policy: index_part.last_aux_file_policy(),
         };
 
         *self = UploadQueue::Initialized(state);
diff --git a/test_runner/regress/test_aux_files.py b/test_runner/regress/test_aux_files.py
new file mode 100644
index 0000000000000..139d49c9f23d1
--- /dev/null
+++ b/test_runner/regress/test_aux_files.py
@@ -0,0 +1,81 @@
+from fixtures.log_helper import log
+from fixtures.neon_fixtures import (
+    NeonEnv,
+    logical_replication_sync,
+)
+
+
+def test_aux_v2_config_switch(neon_simple_env: NeonEnv, vanilla_pg):
+    env = neon_simple_env
+
+    tenant_id = env.initial_tenant
+    timeline_id = env.neon_cli.create_branch("test_aux_v2_config_switch", "empty")
+    endpoint = env.endpoints.create_start(
+        "test_aux_v2_config_switch", config_lines=["log_statement=all"]
+    )
+
+    with env.pageserver.http_client() as client:
+        tenant_config = client.tenant_config(tenant_id).effective_config
+        tenant_config["switch_aux_file_policy"] = "V2"
+        client.set_tenant_config(tenant_id, tenant_config)
+        # aux file v2 is enabled on the write path
+        assert (
+            client.timeline_detail(tenant_id=tenant_id, timeline_id=timeline_id)[
+                "last_aux_file_policy"
+            ]
+            == "Unspecified"
+        )
+    pg_conn = endpoint.connect()
+    cur = pg_conn.cursor()
+
+    cur.execute("create table t(pk integer primary key, payload integer)")
+    cur.execute(
+        "CREATE TABLE replication_example(id SERIAL PRIMARY KEY, somedata int, text varchar(120));"
+    )
+    cur.execute("create publication pub1 for table t, replication_example")
+
+    # now start subscriber, aux files will be created at this point. TODO: find better ways of testing aux files (i.e., neon_test_utils)
+    # instead of going through the full logical replication process.
+    vanilla_pg.start()
+    vanilla_pg.safe_psql("create table t(pk integer primary key, payload integer)")
+    vanilla_pg.safe_psql(
+        "CREATE TABLE replication_example(id SERIAL PRIMARY KEY, somedata int, text varchar(120), testcolumn1 int, testcolumn2 int, testcolumn3 int);"
+    )
+    connstr = endpoint.connstr().replace("'", "''")
+    log.info(f"ep connstr is {endpoint.connstr()}, subscriber connstr {vanilla_pg.connstr()}")
+    vanilla_pg.safe_psql(f"create subscription sub1 connection '{connstr}' publication pub1")
+
+    # Wait logical replication channel to be established
+    logical_replication_sync(vanilla_pg, endpoint)
+    vanilla_pg.stop()
+    endpoint.stop()
+
+    with env.pageserver.http_client() as client:
+        # aux file v2 flag should be enabled at this point
+        assert (
+            client.timeline_detail(tenant_id=tenant_id, timeline_id=timeline_id)[
+                "last_aux_file_policy"
+            ]
+            == "V2"
+        )
+    with env.pageserver.http_client() as client:
+        tenant_config = client.tenant_config(tenant_id).effective_config
+        tenant_config["switch_aux_file_policy"] = "V1"
+        client.set_tenant_config(tenant_id, tenant_config)
+        # the flag should still be enabled
+        assert (
+            client.timeline_detail(tenant_id=tenant_id, timeline_id=timeline_id)[
+                "last_aux_file_policy"
+            ]
+            == "V2"
+        )
+    env.pageserver.restart()
+    with env.pageserver.http_client() as client:
+        # aux file v2 flag should be persisted
+        assert (
+            client.timeline_detail(tenant_id=tenant_id, timeline_id=timeline_id)[
+                "last_aux_file_policy"
+            ]
+            == "V2"
+        )
+    # TODO(chi): test with timeline detach?