diff --git a/pageserver/src/tenant/checks.rs b/pageserver/src/tenant/checks.rs
index 1e8fa8d1d64e..f98356242e1c 100644
--- a/pageserver/src/tenant/checks.rs
+++ b/pageserver/src/tenant/checks.rs
@@ -1,12 +1,15 @@
 use std::collections::BTreeSet;
 
 use itertools::Itertools;
+use pageserver_compaction::helpers::overlaps_with;
 
 use super::storage_layer::LayerName;
 
 /// Checks whether a layer map is valid (i.e., is a valid result of the current compaction algorithm if nothing goes wrong).
 ///
-/// The function checks if we can split the LSN range of a delta layer only at the LSNs of the delta layers. For example,
+/// The function implements a fast path check and a slow path check.
+///
+/// The fast path checks if we can split the LSN range of a delta layer only at the LSNs of the delta layers. For example,
 ///
 /// ```plain
 /// |       |                 |       |
@@ -25,31 +28,47 @@ use super::storage_layer::LayerName;
 /// |       |    |   4   |    |       |
 ///
 /// If layer 2 and 4 contain the same single key, this is also a valid layer map.
+///
+/// However, if a partial compaction is still going on, it is possible that we get a layer map not satisfying the above condition.
+/// Therefore, we fallback to simply check if any of the two delta layers overlap. (See "A slow path...")
 pub fn check_valid_layermap(metadata: &[LayerName]) -> Option<String> {
     let mut lsn_split_point = BTreeSet::new(); // TODO: use a better data structure (range tree / range set?)
     let mut all_delta_layers = Vec::new();
     for name in metadata {
         if let LayerName::Delta(layer) = name {
-            if layer.key_range.start.next() != layer.key_range.end {
-                all_delta_layers.push(layer.clone());
-            }
+            all_delta_layers.push(layer.clone());
         }
     }
     for layer in &all_delta_layers {
-        let lsn_range = &layer.lsn_range;
-        lsn_split_point.insert(lsn_range.start);
-        lsn_split_point.insert(lsn_range.end);
+        if layer.key_range.start.next() != layer.key_range.end {
+            let lsn_range = &layer.lsn_range;
+            lsn_split_point.insert(lsn_range.start);
+            lsn_split_point.insert(lsn_range.end);
+        }
     }
-    for layer in &all_delta_layers {
+    for (idx, layer) in all_delta_layers.iter().enumerate() {
+        if layer.key_range.start.next() == layer.key_range.end {
+            continue;
+        }
         let lsn_range = layer.lsn_range.clone();
         let intersects = lsn_split_point.range(lsn_range).collect_vec();
         if intersects.len() > 1 {
-            let err = format!(
-                "layer violates the layer map LSN split assumption: layer {} intersects with LSN [{}]",
-                layer,
-                intersects.into_iter().map(|lsn| lsn.to_string()).join(", ")
-            );
-            return Some(err);
+            // A slow path to check if the layer intersects with any other delta layer.
+            for (other_idx, other_layer) in all_delta_layers.iter().enumerate() {
+                if other_idx == idx {
+                    // do not check self intersects with self
+                    continue;
+                }
+                if overlaps_with(&layer.lsn_range, &other_layer.lsn_range)
+                    && overlaps_with(&layer.key_range, &other_layer.key_range)
+                {
+                    let err = format!(
+                            "layer violates the layer map LSN split assumption: layer {} intersects with layer {}",
+                            layer, other_layer
+                        );
+                    return Some(err);
+                }
+            }
         }
     }
     None
diff --git a/pageserver/src/tenant/timeline/compaction.rs b/pageserver/src/tenant/timeline/compaction.rs
index a4e8f3952265..01f2a5b170d2 100644
--- a/pageserver/src/tenant/timeline/compaction.rs
+++ b/pageserver/src/tenant/timeline/compaction.rs
@@ -29,6 +29,7 @@ use utils::id::TimelineId;
 use crate::context::{AccessStatsBehavior, RequestContext, RequestContextBuilder};
 use crate::page_cache;
 use crate::statvfs::Statvfs;
+use crate::tenant::checks::check_valid_layermap;
 use crate::tenant::remote_timeline_client::WaitCompletionError;
 use crate::tenant::storage_layer::batch_split_writer::{
     BatchWriterResult, SplitDeltaLayerWriter, SplitImageLayerWriter,
@@ -2156,15 +2157,14 @@ impl Timeline {
 
         // Step 1: construct a k-merge iterator over all layers.
         // Also, verify if the layer map can be split by drawing a horizontal line at every LSN start/end split point.
-        // disable the check for now because we need to adjust the check for partial compactions, will enable later.
-        // let layer_names = job_desc
-        //     .selected_layers
-        //     .iter()
-        //     .map(|layer| layer.layer_desc().layer_name())
-        //     .collect_vec();
-        // if let Some(err) = check_valid_layermap(&layer_names) {
-        //     warn!("gc-compaction layer map check failed because {}, this is normal if partial compaction is not finished yet", err);
-        // }
+        let layer_names = job_desc
+            .selected_layers
+            .iter()
+            .map(|layer| layer.layer_desc().layer_name())
+            .collect_vec();
+        if let Some(err) = check_valid_layermap(&layer_names) {
+            bail!("gc-compaction layer map check failed because {}, cannot proceed with compaction due to potential data loss", err);
+        }
         // The maximum LSN we are processing in this compaction loop
         let end_lsn = job_desc
             .selected_layers
@@ -2546,8 +2546,36 @@ impl Timeline {
         );
 
         // Step 3: Place back to the layer map.
+
+        // First, do a sanity check to ensure the newly-created layer map does not contain overlaps.
+        let all_layers = {
+            let guard = self.layers.read().await;
+            let layer_map = guard.layer_map()?;
+            layer_map.iter_historic_layers().collect_vec()
+        };
+
+        let mut final_layers = all_layers
+            .iter()
+            .map(|layer| layer.layer_name())
+            .collect::<HashSet<_>>();
+        for layer in &layer_selection {
+            final_layers.remove(&layer.layer_desc().layer_name());
+        }
+        for layer in &compact_to {
+            final_layers.insert(layer.layer_desc().layer_name());
+        }
+        let final_layers = final_layers.into_iter().collect_vec();
+
+        // TODO: move this check before we call `finish` on image layer writers. However, this will require us to get the layer name before we finish
+        // the writer, so potentially, we will need a function like `ImageLayerBatchWriter::get_all_pending_layer_keys` to get all the keys that are
+        // in the writer before finalizing the persistent layers. Now we would leave some dangling layers on the disk if the check fails.
+        if let Some(err) = check_valid_layermap(&final_layers) {
+            bail!("gc-compaction layer map check failed after compaction because {}, compaction result not applied to the layer map due to potential data loss", err);
+        }
+
+        // Between the sanity check and this compaction update, there could be new layers being flushed, but it should be fine because we only
+        // operate on L1 layers.
         {
-            // TODO: sanity check if the layer map is valid (i.e., should not have overlaps)
             let mut guard = self.layers.write().await;
             guard
                 .open_mut()?