diff --git a/CHANGELOG.md b/CHANGELOG.md
index 322eb1808..d67b6017f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,25 @@
 - [Rust](https://github.com/moonrepo/rust-plugin/blob/master/CHANGELOG.md)
 - [TOML schema](https://github.com/moonrepo/schema-plugin/blob/master/CHANGELOG.md)
 
+## Unreleased
+
+#### 💥 Breaking
+
+> To ease the migration process, we've added a new migrate command. Simply run `proto migrate v0.24` after upgrading proto!
+
+- Reworked user configured aliases and default/global version.
+  - Moved to `~/.proto/config.toml` (user managed) from `~/.proto/tools/<name>/manifest.json` (internally managed).
+  - Are now stored in the `tools` table (object), indexed by tool name.
+    ```toml
+    [tools.node]
+    default-version = "20.10.0"
+    aliases = { work = "^18" }
+    ```
+
+#### 🚀 Updates
+
+- Added a `proto migrate v0.24` command for migrating aliases/versions. We'll also log a warning if we detect the old configuration.
+
 ## 0.23.2
 
 #### 🐞 Fixes
diff --git a/crates/cli/tests/run_test.rs b/crates/cli/tests/run_test.rs
index 72a7e5ebf..ff0430534 100644
--- a/crates/cli/tests/run_test.rs
+++ b/crates/cli/tests/run_test.rs
@@ -106,10 +106,7 @@ mod run {
         fs::remove_file(temp.path().join(".prototools")).unwrap();
 
         // Global version
-        temp.create_file(
-            "tools/node/manifest.json",
-            r#"{ "default_version": "19.0.0", "installed_versions": ["19.0.0"] }"#,
-        );
+        temp.create_file("config.toml", "[tools.node]\ndefault-version = \"19.0.0\"");
 
         let mut cmd = create_proto_command(temp.path());
         let assert = cmd
@@ -121,7 +118,7 @@ mod run {
 
         assert.stdout(predicate::str::contains("19.0.0"));
 
-        fs::remove_file(temp.path().join("tools/node/manifest.json")).unwrap();
+        fs::remove_file(temp.path().join("config.toml")).unwrap();
     }
 
     // This test fails in Windows for some reason, but works fine with `cargo run`...
diff --git a/crates/core/src/proto.rs b/crates/core/src/proto.rs
index e10f0d47c..8fd727158 100644
--- a/crates/core/src/proto.rs
+++ b/crates/core/src/proto.rs
@@ -82,11 +82,11 @@ impl ProtoEnvironment {
 
     pub fn load_user_config(&self) -> miette::Result<&UserConfig> {
         self.user_config.get_or_try_init(|| {
-            if self.test_mode || env::var("PROTO_TEST_USER_CONFIG").is_ok() {
-                Ok(UserConfig::default())
-            } else {
-                UserConfig::load_from(&self.root)
-            }
+            // if self.test_mode || env::var("PROTO_TEST_USER_CONFIG").is_ok() {
+            //     Ok(UserConfig::default())
+            // } else {
+            UserConfig::load_from(&self.root)
+            // }
         })
     }
 
diff --git a/crates/core/src/tool_manifest.rs b/crates/core/src/tool_manifest.rs
index fb017cce8..0019aa995 100644
--- a/crates/core/src/tool_manifest.rs
+++ b/crates/core/src/tool_manifest.rs
@@ -1,12 +1,13 @@
 use crate::helpers::{read_json_file_with_lock, write_json_file_with_lock};
 use serde::{Deserialize, Serialize};
+use starbase_styles::color;
 use std::{
     collections::{BTreeMap, HashSet},
     env,
     path::{Path, PathBuf},
     time::SystemTime,
 };
-use tracing::{debug, info};
+use tracing::{debug, info, warn};
 use version_spec::*;
 
 fn now() -> u128 {
@@ -73,6 +74,22 @@ impl ToolManifest {
 
         manifest.path = path.to_owned();
 
+        #[allow(deprecated)]
+        if !manifest.aliases.is_empty() {
+            warn!(
+                "Found legacy aliases in tool manifest, please run {} to migrate them",
+                color::shell("proto migrate v0.24")
+            );
+        }
+
+        #[allow(deprecated)]
+        if manifest.default_version.is_some() {
+            warn!(
+                "Found legacy default version in tool manifest, please run {} to migrate it",
+                color::shell("proto migrate v0.24")
+            );
+        }
+
         Ok(manifest)
     }
 
@@ -125,14 +142,7 @@ impl ToolManifest {
     }
 
     pub fn track_used_at(&mut self, version: VersionSpec) {
-        self.versions
-            .entry(version)
-            .and_modify(|v| {
-                v.last_used_at = Some(now());
-            })
-            .or_insert(ToolManifestVersion {
-                last_used_at: Some(now()),
-                ..ToolManifestVersion::default()
-            });
+        let entry = self.versions.entry(version).or_default();
+        entry.last_used_at = Some(now());
     }
 }
diff --git a/crates/core/src/version_detector.rs b/crates/core/src/version_detector.rs
index 97d41959e..68c16709d 100644
--- a/crates/core/src/version_detector.rs
+++ b/crates/core/src/version_detector.rs
@@ -126,7 +126,7 @@ pub async fn detect_version(
         return Ok(candidate);
     }
 
-    // Env var takes highest priorit
+    // Env var takes highest priority
     let env_var = format!("{}_VERSION", tool.get_env_var_prefix());
 
     if let Ok(session_version) = env::var(&env_var) {
@@ -170,18 +170,22 @@ pub async fn detect_version(
     // If still no version, load the global version
     trace!(
         tool = tool.id.as_str(),
-        "Attempting to use global version from manifest",
+        "Attempting to use global version from user config",
     );
 
-    if let Some(global_version) = &tool.manifest.default_version {
-        debug!(
-            tool = tool.id.as_str(),
-            version = global_version.to_string(),
-            file = ?tool.manifest.path,
-            "Detected global version from manifest",
-        );
+    let user_config = tool.proto.load_user_config()?;
+
+    if let Some(tool_user_config) = user_config.tools.get(&tool.id) {
+        if let Some(global_version) = &tool_user_config.default_version {
+            debug!(
+                tool = tool.id.as_str(),
+                version = global_version.to_string(),
+                file = ?user_config.path,
+                "Detected global version from user config",
+            );
 
-        return Ok(global_version.to_owned());
+            return Ok(global_version.to_owned());
+        }
     }
 
     // We didn't find anything!