diff --git a/lib/gdk/postgresql_upgrader.rb b/lib/gdk/postgresql_upgrader.rb
index 725dd8df5e432229583ae51e110cf7ef7730ab6d..a70981149c2fe38a41f2494414482acab05377f6 100644
--- a/lib/gdk/postgresql_upgrader.rb
+++ b/lib/gdk/postgresql_upgrader.rb
@@ -107,8 +107,8 @@ def rename_current_data_dir_back
     def pgvector_setup
       return unless config.gitlab.rails.databases.embedding.enabled?
 
-      GDK::Output.info "Running 'make pgvector-setup'.."
-      run!('make pgvector-setup', config.gdk_root)
+      GDK::Output.info "Running 'make pgvector-clean pgvector-setup'.."
+      run!('make pgvector-clean pgvector-setup', config.gdk_root)
     end
 
     def pg_upgrade