diff --git a/db/migrate/20250923074051_add_default_value_to_workspace_desired_config_generator_version.rb b/db/migrate/20250923074051_add_default_value_to_workspace_desired_config_generator_version.rb
new file mode 100644
index 0000000000000000000000000000000000000000..d1d29fce30a3041251b90c055f97338c09b7bd68
--- /dev/null
+++ b/db/migrate/20250923074051_add_default_value_to_workspace_desired_config_generator_version.rb
@@ -0,0 +1,13 @@
+# frozen_string_literal: true
+
+class AddDefaultValueToWorkspaceDesiredConfigGeneratorVersion < Gitlab::Database::Migration[2.3]
+  milestone '18.5'
+
+  def up
+    change_column_default :workspaces, :desired_config_generator_version, 3
+  end
+
+  def down
+    change_column_default :workspaces, :desired_config_generator_version, nil
+  end
+end
diff --git a/db/migrate/20251001180828_add_index_on_workspace_desired_config_generator_version.rb b/db/migrate/20251001180828_add_index_on_workspace_desired_config_generator_version.rb
new file mode 100644
index 0000000000000000000000000000000000000000..2f5943e6679d78c17cfe0150e2d5ef19efd78b8d
--- /dev/null
+++ b/db/migrate/20251001180828_add_index_on_workspace_desired_config_generator_version.rb
@@ -0,0 +1,22 @@
+# frozen_string_literal: true
+
+# See https://docs.gitlab.com/ee/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+class AddIndexOnWorkspaceDesiredConfigGeneratorVersion < Gitlab::Database::Migration[2.3]
+  milestone '18.5'
+  disable_ddl_transaction!
+
+  def up
+    add_concurrent_index(
+      :workspaces,
+      :id,
+      where: "desired_config_generator_version IS NULL",
+      name: "idx_workspaces_null_config_version_id"
+    )
+  end
+
+  def down
+    remove_concurrent_index_by_name :workspaces, name: "idx_workspaces_null_config_version_id"
+  end
+end
diff --git a/db/post_migrate/20251001180830_update_nil_desired_config_generator_version_workspace.rb b/db/post_migrate/20251001180830_update_nil_desired_config_generator_version_workspace.rb
new file mode 100644
index 0000000000000000000000000000000000000000..fd5741415a19c09ae1de651600ce1c48b2cdf102
--- /dev/null
+++ b/db/post_migrate/20251001180830_update_nil_desired_config_generator_version_workspace.rb
@@ -0,0 +1,21 @@
+# frozen_string_literal: true
+
+class UpdateNilDesiredConfigGeneratorVersionWorkspace < Gitlab::Database::Migration[2.3]
+  disable_ddl_transaction!
+  restrict_gitlab_migration gitlab_schema: :gitlab_main
+  milestone '18.5'
+
+  def up
+    workspaces = define_batchable_model('workspaces')
+
+    workspaces
+      .where(desired_config_generator_version: nil)
+      .each_batch(of: 50) do |batch|
+      batch.update_all(desired_config_generator_version: 3)
+    end
+  end
+
+  def down
+    # no-op
+  end
+end
diff --git a/db/schema_migrations/20250923074051 b/db/schema_migrations/20250923074051
new file mode 100644
index 0000000000000000000000000000000000000000..7a6ba4c41a1361572889c301a266eb9a9feadce9
--- /dev/null
+++ b/db/schema_migrations/20250923074051
@@ -0,0 +1 @@
+89070fe81a15bdc3f7a7918db13ca5ddf1cd585b196c21ca696173c3e18cf52e
\ No newline at end of file
diff --git a/db/schema_migrations/20251001180828 b/db/schema_migrations/20251001180828
new file mode 100644
index 0000000000000000000000000000000000000000..7baab5be2bd8b7141c08861ad34e861b0299fabd
--- /dev/null
+++ b/db/schema_migrations/20251001180828
@@ -0,0 +1 @@
+2aea40daf2bbc511b242523e9f42d1a87eea01d59dfcb1b36760dfad066a659e
\ No newline at end of file
diff --git a/db/schema_migrations/20251001180830 b/db/schema_migrations/20251001180830
new file mode 100644
index 0000000000000000000000000000000000000000..97ef1410f5952d5c3c490eccfdae768b7778a0ca
--- /dev/null
+++ b/db/schema_migrations/20251001180830
@@ -0,0 +1 @@
+8f8b2a331aa56032628eee28b07756bf83b1501a42665f99a82bdb5cd03338ad
\ No newline at end of file
diff --git a/db/structure.sql b/db/structure.sql
index 211863b3de8a53014ad8a5c44f7a3f301a9b82a1..110754bdce941565b6f1f22787680c614e386dde 100644
--- a/db/structure.sql
+++ b/db/structure.sql
@@ -29315,7 +29315,7 @@ CREATE TABLE workspaces (
     url_prefix text,
     url_query_string text,
     workspaces_agent_config_version integer NOT NULL,
-    desired_config_generator_version integer,
+    desired_config_generator_version integer DEFAULT 3,
     project_ref text,
     actual_state_updated_at timestamp with time zone NOT NULL,
     CONSTRAINT check_15543fb0fa CHECK ((char_length(name) <= 64)),
@@ -38164,6 +38164,8 @@ CREATE INDEX idx_wi_type_custom_lifecycles_on_work_item_type_id ON work_item_typ
 
 CREATE INDEX idx_workflows_status_updated_at_id ON duo_workflows_workflows USING btree (status, updated_at, id);
 
+CREATE INDEX idx_workspaces_null_config_version_id ON workspaces USING btree (id) WHERE (desired_config_generator_version IS NULL);
+
 CREATE INDEX idx_zoekt_last_indexed_at_gt_used_storage_bytes_updated_at ON zoekt_indices USING btree (used_storage_bytes_updated_at) WHERE (last_indexed_at >= used_storage_bytes_updated_at);
 
 CREATE INDEX idx_zoekt_repositories_on_zoekt_index_id_and_size_bytes ON zoekt_repositories USING btree (zoekt_index_id, size_bytes);