diff --git a/godot-core/src/meta/class_id.rs b/godot-core/src/meta/class_id.rs
index d8df04fab..efaca595e 100644
--- a/godot-core/src/meta/class_id.rs
+++ b/godot-core/src/meta/class_id.rs
@@ -309,8 +309,17 @@ impl ClassIdCache {
     }
 
     fn clear(&mut self) {
-        self.entries.clear();
+        // There are two types of hot reload:
+        // - dylib reload (dylib mtime newer): the old dylib is unloaded and the new one is loaded
+        // - .gdextension reload (.gdextension mtime newer): the existing dylib is re-initialized without unloading
+        //
+        // .gdextension reload keeps existing ClassIds alive with each id being an index into entries.
+        // To account for this, we preserve the backing data for existing entries, but drop the cached Godot
+        // StringNames and the TypeId lookup so they can be rebuilt.
+        for entry in &mut self.entries {
+            entry.godot_str = OnceCell::new();
+        }
+
         self.type_to_index.clear();
-        self.string_to_index.clear();
     }
 }
diff --git a/godot-ffi/src/lib.rs b/godot-ffi/src/lib.rs
index a1e2e4156..fdd87509d 100644
--- a/godot-ffi/src/lib.rs
+++ b/godot-ffi/src/lib.rs
@@ -284,7 +284,15 @@ pub unsafe fn initialize(
 /// # Safety
 /// See [`initialize`].
 pub unsafe fn deinitialize() {
-    deinitialize_binding()
+    deinitialize_binding();
+
+    // Clear the main thread ID to allow re-initialization during hot reload.
+    #[cfg(not(wasm_nothreads))]
+    {
+        if MAIN_THREAD_ID.is_initialized() {
+            MAIN_THREAD_ID.clear();
+        }
+    }
 }
 
 fn print_preamble(version: GDExtensionGodotVersion) {
diff --git a/itest/hot-reload/godot/run-test.sh b/itest/hot-reload/godot/run-test.sh
index 828f8e583..58b171979 100755
--- a/itest/hot-reload/godot/run-test.sh
+++ b/itest/hot-reload/godot/run-test.sh
@@ -54,6 +54,11 @@ cargo build -p hot-reload $cargoArgs
 # Wait briefly so artifacts are present on file system.
 sleep 0.5
 
+# ----------------------------------------------------------------
+# Test Case 1: Update Rust source and compile to trigger reload.
+# ----------------------------------------------------------------
+
+echo "[Bash]      Scenario 1: Reload after updating Rust source..."
 $GODOT4_BIN -e --headless --path $rel &
 godotPid=$!
 echo "[Bash]      Wait for Godot ready (PID $godotPid)..."
@@ -70,6 +75,32 @@ echo "[Bash]      Wait for Godot exit..."
 wait $godotPid
 status=$?
 echo "[Bash]      Godot (PID $godotPid) has completed with status $status."
+if [[ $status -ne 0 ]]; then
+  exit $status
+fi
+
+# ----------------------------------------------------------------
+# Test Case 2: Touch the .gdextension file to trigger reload.
+# ----------------------------------------------------------------
+godotPid=0
+
+echo "[Bash]      Scenario 2: Reload after touching rust.gdextension..."
+$GODOT4_BIN -e --headless --path $rel &
+godotPid=$!
+echo "[Bash]      Wait for Godot ready (PID $godotPid)..."
 
+$GODOT4_BIN --headless --no-header --script ReloadOrchestrator.gd -- await
+
+# update timestamp to trigger reload
+touch "$rel/rust.gdextension"
 
+$GODOT4_BIN --headless --no-header --script ReloadOrchestrator.gd -- notify
 
+echo "[Bash]      Wait for Godot exit (dirty scenario)..."
+wait $godotPid
+status=$?
+echo "[Bash]      Godot (PID $godotPid) has completed with status $status."
+if [[ $status -ne 0 ]]; then
+  exit $status
+fi
+godotPid=0