diff --git a/backend/app/core/database.py b/backend/app/core/database.py
index 13600ff64..5cc855907 100644
--- a/backend/app/core/database.py
+++ b/backend/app/core/database.py
@@ -1530,6 +1530,17 @@ async def run_migrations(conn):
         "CREATE INDEX IF NOT EXISTS ix_library_files_deleted_at ON library_files(deleted_at)",
     )
 
+    # Legacy SQLite installs created `settings` without a UNIQUE constraint on `key`,
+    # so `INSERT OR IGNORE` below silently degrades to a plain INSERT and dupes rows on
+    # every restart. Dedupe (keep lowest id per key) and add the missing unique index
+    # before seeding. Safe/idempotent on both dialects — fresh installs already have
+    # no dupes and `create_all` already emits the index.
+    await _safe_execute(
+        conn,
+        "DELETE FROM settings WHERE id NOT IN (SELECT MIN(id) FROM settings GROUP BY key)",
+    )
+    await _safe_execute(conn, "CREATE UNIQUE INDEX IF NOT EXISTS ix_settings_key ON settings(key)")
+
     # Seed default settings keys that must exist on fresh install
     default_settings = [
         ("advanced_auth_enabled", "false"),