diff --git a/compute_tools/src/extension_server.rs b/compute_tools/src/extension_server.rs
index da5d519ab5..1b5e4cf974 100644
--- a/compute_tools/src/extension_server.rs
+++ b/compute_tools/src/extension_server.rs
@@ -156,7 +156,7 @@ pub async fn get_available_extensions(
     let ext_index_full = serde_json::from_slice::<Index>(&ext_idx_buffer)?;
     let mut enabled_extensions = ext_index_full.public_extensions;
     enabled_extensions.extend_from_slice(custom_extensions);
-    let library_index = ext_index_full.library_index;
+    let mut library_index = ext_index_full.library_index;
     let all_extension_data = ext_index_full.extension_data;
     info!("library_index: {:?}", library_index);
 
@@ -179,6 +179,8 @@ pub async fn get_available_extensions(
                 file_create_tasks.push(tokio::fs::write(control_path, control_contents));
             } else {
                 warn!("control file {:?} exists both locally and remotely. ignoring the remote version.", control_file);
+                // also delete this from library index
+                library_index.retain(|_, value| value != extension_name);
             }
         }
     }