diff --git a/packages/backend/server/scripts/repair-pgvector-embedding-tables.sql b/packages/backend/server/scripts/repair-pgvector-embedding-tables.sql
new file mode 100644
index 000000000..4a26ba7fb
--- /dev/null
+++ b/packages/backend/server/scripts/repair-pgvector-embedding-tables.sql
@@ -0,0 +1,143 @@
+DO $$
+DECLARE
+  has_hnsw BOOLEAN;
+BEGIN
+  IF NOT EXISTS (SELECT 1 FROM pg_extension WHERE extname = 'vector') THEN
+    BEGIN
+      CREATE EXTENSION IF NOT EXISTS "vector";
+    EXCEPTION
+      WHEN OTHERS THEN
+        RAISE NOTICE 'pgvector extension is not available. Skip repairing copilot embedding tables.';
+        RETURN;
+    END;
+  END IF;
+
+  SELECT EXISTS (SELECT 1 FROM pg_am WHERE amname = 'hnsw') INTO has_hnsw;
+
+  IF NOT has_hnsw THEN
+    RAISE NOTICE 'pgvector HNSW index access method is not available. Skip repairing copilot embedding indexes.';
+  END IF;
+
+  IF to_regclass('public.ai_contexts') IS NOT NULL THEN
+    CREATE TABLE IF NOT EXISTS "ai_context_embeddings" (
+      "id" VARCHAR NOT NULL,
+      "context_id" VARCHAR NOT NULL,
+      "file_id" VARCHAR NOT NULL,
+      "chunk" INTEGER NOT NULL,
+      "content" VARCHAR NOT NULL,
+      "embedding" vector(1024) NOT NULL,
+      "created_at" TIMESTAMPTZ(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+      "updated_at" TIMESTAMPTZ(3) NOT NULL,
+      CONSTRAINT "ai_context_embeddings_pkey" PRIMARY KEY ("id")
+    );
+
+    IF has_hnsw THEN
+      CREATE INDEX IF NOT EXISTS "ai_context_embeddings_idx"
+        ON "ai_context_embeddings" USING hnsw ("embedding" vector_cosine_ops);
+    END IF;
+    CREATE UNIQUE INDEX IF NOT EXISTS "ai_context_embeddings_context_id_file_id_chunk_key"
+      ON "ai_context_embeddings"("context_id", "file_id", "chunk");
+
+    IF NOT EXISTS (
+      SELECT 1 FROM pg_constraint
+      WHERE conname = 'ai_context_embeddings_context_id_fkey'
+        AND conrelid = 'public.ai_context_embeddings'::regclass
+    ) THEN
+      ALTER TABLE "ai_context_embeddings"
+        ADD CONSTRAINT "ai_context_embeddings_context_id_fkey"
+        FOREIGN KEY ("context_id") REFERENCES "ai_contexts"("id")
+        ON DELETE CASCADE ON UPDATE CASCADE;
+    END IF;
+  END IF;
+
+  IF to_regclass('public.snapshots') IS NOT NULL THEN
+    CREATE TABLE IF NOT EXISTS "ai_workspace_embeddings" (
+      "workspace_id" VARCHAR NOT NULL,
+      "doc_id" VARCHAR NOT NULL,
+      "chunk" INTEGER NOT NULL,
+      "content" VARCHAR NOT NULL,
+      "embedding" vector(1024) NOT NULL,
+      "created_at" TIMESTAMPTZ(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+      "updated_at" TIMESTAMPTZ(3) NOT NULL,
+      CONSTRAINT "ai_workspace_embeddings_pkey"
+        PRIMARY KEY ("workspace_id", "doc_id", "chunk")
+    );
+
+    IF has_hnsw THEN
+      CREATE INDEX IF NOT EXISTS "ai_workspace_embeddings_idx"
+        ON "ai_workspace_embeddings" USING hnsw ("embedding" vector_cosine_ops);
+    END IF;
+
+    IF NOT EXISTS (
+      SELECT 1 FROM pg_constraint
+      WHERE conname = 'ai_workspace_embeddings_workspace_id_doc_id_fkey'
+        AND conrelid = 'public.ai_workspace_embeddings'::regclass
+    ) THEN
+      ALTER TABLE "ai_workspace_embeddings"
+        ADD CONSTRAINT "ai_workspace_embeddings_workspace_id_doc_id_fkey"
+        FOREIGN KEY ("workspace_id", "doc_id")
+        REFERENCES "snapshots"("workspace_id", "guid")
+        ON DELETE CASCADE ON UPDATE CASCADE;
+    END IF;
+  END IF;
+
+  IF to_regclass('public.ai_workspace_files') IS NOT NULL THEN
+    CREATE TABLE IF NOT EXISTS "ai_workspace_file_embeddings" (
+      "workspace_id" VARCHAR NOT NULL,
+      "file_id" VARCHAR NOT NULL,
+      "chunk" INTEGER NOT NULL,
+      "content" VARCHAR NOT NULL,
+      "embedding" vector(1024) NOT NULL,
+      "created_at" TIMESTAMPTZ(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+      CONSTRAINT "ai_workspace_file_embeddings_pkey"
+        PRIMARY KEY ("workspace_id", "file_id", "chunk")
+    );
+
+    IF has_hnsw THEN
+      CREATE INDEX IF NOT EXISTS "ai_workspace_file_embeddings_idx"
+        ON "ai_workspace_file_embeddings" USING hnsw ("embedding" vector_cosine_ops);
+    END IF;
+
+    IF NOT EXISTS (
+      SELECT 1 FROM pg_constraint
+      WHERE conname = 'ai_workspace_file_embeddings_workspace_id_file_id_fkey'
+        AND conrelid = 'public.ai_workspace_file_embeddings'::regclass
+    ) THEN
+      ALTER TABLE "ai_workspace_file_embeddings"
+        ADD CONSTRAINT "ai_workspace_file_embeddings_workspace_id_file_id_fkey"
+        FOREIGN KEY ("workspace_id", "file_id")
+        REFERENCES "ai_workspace_files"("workspace_id", "file_id")
+        ON DELETE CASCADE ON UPDATE CASCADE;
+    END IF;
+  END IF;
+
+  IF to_regclass('public.blobs') IS NOT NULL THEN
+    CREATE TABLE IF NOT EXISTS "ai_workspace_blob_embeddings" (
+      "workspace_id" VARCHAR NOT NULL,
+      "blob_id" VARCHAR NOT NULL,
+      "chunk" INTEGER NOT NULL,
+      "content" VARCHAR NOT NULL,
+      "embedding" vector(1024) NOT NULL,
+      "created_at" TIMESTAMPTZ(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+      CONSTRAINT "ai_workspace_blob_embeddings_pkey"
+        PRIMARY KEY ("workspace_id", "blob_id", "chunk")
+    );
+
+    IF has_hnsw THEN
+      CREATE INDEX IF NOT EXISTS "ai_workspace_blob_embeddings_idx"
+        ON "ai_workspace_blob_embeddings" USING hnsw ("embedding" vector_cosine_ops);
+    END IF;
+
+    IF NOT EXISTS (
+      SELECT 1 FROM pg_constraint
+      WHERE conname = 'ai_workspace_blob_embeddings_workspace_id_blob_id_fkey'
+        AND conrelid = 'public.ai_workspace_blob_embeddings'::regclass
+    ) THEN
+      ALTER TABLE "ai_workspace_blob_embeddings"
+        ADD CONSTRAINT "ai_workspace_blob_embeddings_workspace_id_blob_id_fkey"
+        FOREIGN KEY ("workspace_id", "blob_id")
+        REFERENCES "blobs"("workspace_id", "key")
+        ON DELETE CASCADE ON UPDATE CASCADE;
+    END IF;
+  END IF;
+END $$;
diff --git a/packages/backend/server/scripts/self-host-predeploy.js b/packages/backend/server/scripts/self-host-predeploy.js
index f6d829212..531dd00c1 100644
--- a/packages/backend/server/scripts/self-host-predeploy.js
+++ b/packages/backend/server/scripts/self-host-predeploy.js
@@ -38,9 +38,32 @@ function prepare() {
   }
 }
 
-function runPredeployScript() {
-  console.log('running predeploy script.');
-  execSync('yarn predeploy', {
+function runPrismaMigrations() {
+  console.log('running prisma migrations.');
+  execSync('yarn prisma migrate deploy', {
+    encoding: 'utf-8',
+    env: process.env,
+    stdio: 'inherit',
+  });
+}
+
+function repairPgvectorEmbeddingTables() {
+  console.log('repairing copilot pgvector embedding tables.');
+  const sql = fs.readFileSync(
+    path.join(import.meta.dirname, 'repair-pgvector-embedding-tables.sql'),
+    'utf-8'
+  );
+  execSync('yarn prisma db execute --stdin --schema schema.prisma', {
+    encoding: 'utf-8',
+    env: process.env,
+    input: sql,
+    stdio: ['pipe', 'inherit', 'inherit'],
+  });
+}
+
+function runDataMigrations() {
+  console.log('running data migrations.');
+  execSync('yarn cli run', {
     encoding: 'utf-8',
     env: process.env,
     stdio: 'inherit',
@@ -85,4 +108,6 @@ function fixFailedMigrations() {
 
 prepare();
 fixFailedMigrations();
-runPredeployScript();
+runPrismaMigrations();
+repairPgvectorEmbeddingTables();
+runDataMigrations();