diff --git a/crates/pod-store/src/lib.rs b/crates/pod-store/src/lib.rs
index 25422af7..e757120c 100644
--- a/crates/pod-store/src/lib.rs
+++ b/crates/pod-store/src/lib.rs
@@ -165,16 +165,30 @@ pub trait PodMetadataStore: Send + Sync {
         Ok(metadata)
     }
 
-    /// Set the active pointer while preserving spawned children and manifest snapshot.
+    /// Set the active pointer while preserving spawned children, workspace ownership, and manifest snapshot.
     fn set_active(
         &self,
         pod_name: &str,
         active: Option<PodActiveSegmentRef>,
         resolved_manifest_snapshot: Option<serde_json::Value>,
+    ) -> Result<PodMetadata, PodStoreError> {
+        self.set_active_with_workspace_root(pod_name, active, resolved_manifest_snapshot, None)
+    }
+
+    /// Set the active pointer and workspace ownership while preserving unrelated fields.
+    fn set_active_with_workspace_root(
+        &self,
+        pod_name: &str,
+        active: Option<PodActiveSegmentRef>,
+        resolved_manifest_snapshot: Option<serde_json::Value>,
+        workspace_root: Option<PathBuf>,
     ) -> Result<PodMetadata, PodStoreError> {
         self.update_by_name(pod_name, |metadata| {
             metadata.active = active;
             metadata.resolved_manifest_snapshot = resolved_manifest_snapshot;
+            if let Some(workspace_root) = workspace_root {
+                metadata.workspace_root = Some(workspace_root);
+            }
         })
     }
 
diff --git a/crates/pod/src/pod.rs b/crates/pod/src/pod.rs
index abeece58..9c4da1a8 100644
--- a/crates/pod/src/pod.rs
+++ b/crates/pod/src/pod.rs
@@ -72,10 +72,11 @@ where
     let store = store.clone();
     Arc::new(move |metadata| {
         store
-            .set_active(
+            .set_active_with_workspace_root(
                 &metadata.pod_name,
                 metadata.active,
                 metadata.resolved_manifest_snapshot,
+                metadata.workspace_root,
             )
             .map(|_| ())
     })
@@ -5236,6 +5237,24 @@ permission = "write"
 mod pod_metadata_restore_manifest_tests {
     use super::*;
 
+    #[test]
+    fn metadata_writer_persists_workspace_root_through_store_update() {
+        let temp = tempfile::tempdir().unwrap();
+        let store = pod_store::FsPodStore::new(temp.path().join("pods")).unwrap();
+        let workspace_root = temp.path().join("workspace-root");
+        std::fs::create_dir_all(&workspace_root).unwrap();
+        let writer = pod_metadata_writer_for_store(&store);
+
+        writer(PodMetadata::new("runtime-pod", None).with_workspace_root(workspace_root.clone()))
+            .unwrap();
+
+        let stored = store.read_by_name("runtime-pod").unwrap().unwrap();
+        assert_eq!(
+            stored.workspace_root.as_deref(),
+            Some(workspace_root.as_path())
+        );
+    }
+
     #[test]
     fn snapshot_preserves_saved_scope_over_current_manifest() {
         let saved = PodManifest::from_toml(