diff --git a/src/snapshot_middleware/lua.rs b/src/snapshot_middleware/lua.rs
index 6f3040e9..077a9b4b 100644
--- a/src/snapshot_middleware/lua.rs
+++ b/src/snapshot_middleware/lua.rs
@@ -128,10 +128,16 @@ pub fn snapshot_lua_init(
     let mut init_snapshot =
         snapshot_lua(context, vfs, init_path, &dir_snapshot.name, script_type)?.unwrap();
 
+    // Preserve the init script's instigating_source (the actual file path)
+    // before copying the directory's metadata (which has the folder path)
+    let script_instigating_source = init_snapshot.metadata.instigating_source.take();
+
     init_snapshot.children = dir_snapshot.children;
     init_snapshot.metadata = dir_snapshot.metadata;
-    // The directory snapshot middleware includes all possible init paths
-    // so we don't need to add it here.
+
+    // Restore the init script's instigating_source so two-way sync writes
+    // to the actual file (e.g., init.luau) instead of the directory
+    init_snapshot.metadata.instigating_source = script_instigating_source;
 
     DirectoryMetadata::read_and_apply_all(vfs, folder_path, &mut init_snapshot)?;
 
diff --git a/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs.snap b/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs.snap
index 6175f588..45416fff 100644
--- a/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs.snap
+++ b/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs.snap
@@ -6,7 +6,7 @@ snapshot_id: "00000000000000000000000000000000"
 metadata:
   ignore_unknown_instances: false
   instigating_source:
-    Path: /root
+    Path: /root/init.lua
   relevant_paths:
     - /root
     - /root/init.lua
diff --git a/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs_with_meta.snap b/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs_with_meta.snap
index 23a7f6b1..736985d4 100644
--- a/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs_with_meta.snap
+++ b/src/snapshot_middleware/snapshots/librojo__snapshot_middleware__lua__test__init_module_from_vfs_with_meta.snap
@@ -6,7 +6,7 @@ snapshot_id: "00000000000000000000000000000000"
 metadata:
   ignore_unknown_instances: false
   instigating_source:
-    Path: /root
+    Path: /root/init.lua
   relevant_paths:
     - /root
     - /root/init.lua