diff --git a/server/src/chat/transport/matrix/delete.rs b/server/src/chat/transport/matrix/delete.rs
index af78db2f..4e2e2b38 100644
--- a/server/src/chat/transport/matrix/delete.rs
+++ b/server/src/chat/transport/matrix/delete.rs
@@ -103,6 +103,7 @@ pub async fn handle_delete(
     // Delete from the content store and CRDT.
     crate::db::delete_content(&story_id);
     crate::db::delete_item(&story_id);
+    let _ = crate::crdt_state::evict_item(&story_id);
 
     // Build the response.
     let stage_label = stage_display_name(&stage);
@@ -244,6 +245,53 @@ mod tests {
         );
     }
 
+    #[tokio::test]
+    async fn handle_delete_writes_crdt_tombstone() {
+        // Initialise the global CRDT singleton (no-op if already done).
+        crate::crdt_state::init_for_test();
+
+        let story_id = "9977_story_crdt_tombstone_check";
+        let story_number = "9977";
+
+        // Seed in CRDT.
+        crate::crdt_state::write_item(
+            story_id,
+            "1_backlog",
+            Some("CRDT Tombstone Check"),
+            None,
+            None,
+            None,
+            None,
+            None,
+            None,
+            None,
+        );
+
+        // Seed in content store so find_story_by_number can resolve it.
+        crate::db::ensure_content_store();
+        crate::db::write_item_with_content(
+            story_id,
+            "1_backlog",
+            "---\nname: CRDT Tombstone Check\n---\n\n# Story 9977\n",
+        );
+
+        let tmp = tempfile::tempdir().unwrap();
+        let project_root = tmp.path();
+        let agents = std::sync::Arc::new(crate::agents::AgentPool::new_test(3002));
+        handle_delete("Timmy", story_number, project_root, &agents).await;
+
+        // The CRDT dump includes tombstoned entries — verify is_deleted = true.
+        let dump = crate::crdt_state::dump_crdt_state(Some(story_id));
+        let deleted = dump
+            .items
+            .iter()
+            .any(|i| i.story_id.as_deref() == Some(story_id) && i.is_deleted);
+        assert!(
+            deleted,
+            "CRDT must show is_deleted=true for '{story_id}' after handle_delete"
+        );
+    }
+
     #[tokio::test]
     async fn handle_delete_removes_story_file_and_confirms() {
         let tmp = tempfile::tempdir().unwrap();
diff --git a/server/src/crdt_state/read.rs b/server/src/crdt_state/read.rs
index cab05869..99f51ab0 100644
--- a/server/src/crdt_state/read.rs
+++ b/server/src/crdt_state/read.rs
@@ -249,8 +249,13 @@ pub fn evict_item(story_id: &str) -> Result<(), String> {
 
     // Resolve the item's OpId before the closure (the closure will mutably
     // borrow `state`, so we can't access `state.crdt.doc.items` from inside).
+    //
+    // `rebuild_index` uses `items.iter()` which skips the invisible ROOT
+    // sentinel, so `idx` is a 0-based visible-item position.  `id_at` counts
+    // ALL non-deleted ops including the sentinel at position 0, so we must
+    // add 1 to translate from visible-item position to `id_at` position.
     let item_id =
-        state.crdt.doc.items.id_at(idx).ok_or_else(|| {
+        state.crdt.doc.items.id_at(idx + 1).ok_or_else(|| {
             format!("Item index {idx} for '{story_id}' did not resolve to an OpId")
         })?;