diff --git a/extensions/ql-vscode/src/databases.ts b/extensions/ql-vscode/src/databases.ts
index 269d8a94e..7cd26bb28 100644
--- a/extensions/ql-vscode/src/databases.ts
+++ b/extensions/ql-vscode/src/databases.ts
@@ -811,6 +811,9 @@ export class DatabaseManager extends DisposableObject {
       vscode.workspace.updateWorkspaceFolders(folderIndex, 1);
     }
 
+    // Remove this database item from the allow-list
+    await this.deregisterDatabase(progress, token, item);
+
     // Delete folder from file system only if it is controlled by the extension
     if (this.isExtensionControlledLocation(item.databaseUri)) {
       logger.log('Deleting database from filesystem.');
@@ -819,9 +822,6 @@ export class DatabaseManager extends DisposableObject {
         e => logger.log(`Failed to delete '${item.databaseUri.fsPath}'. Reason: ${e.message}`));
     }
 
-    // Remove this database item from the allow-list
-    await this.deregisterDatabase(progress, token, item);
-
     // note that we use undefined as the item in order to reset the entire tree
     this._onDidChangeDatabaseItem.fire({
       item: undefined,