diff --git a/db/post_migrate/20251014140356_remove_workspace_desired_config_generator_version_column.rb b/db/post_migrate/20251014140356_remove_workspace_desired_config_generator_version_column.rb
new file mode 100644
index 0000000000000000000000000000000000000000..d4e58da492222b5935102c740e344d18f6c565c7
--- /dev/null
+++ b/db/post_migrate/20251014140356_remove_workspace_desired_config_generator_version_column.rb
@@ -0,0 +1,20 @@
+# frozen_string_literal: true
+
+class RemoveWorkspaceDesiredConfigGeneratorVersionColumn < Gitlab::Database::Migration[2.3]
+  disable_ddl_transaction!
+  milestone '18.6'
+
+  def up
+    remove_column :workspaces, :desired_config_generator_version, if_exists: true
+  end
+
+  def down
+    add_column :workspaces, :desired_config_generator_version, :integer, default: 3, if_not_exists: true
+    add_concurrent_index(
+      :workspaces,
+      :id,
+      where: "desired_config_generator_version IS NULL",
+      name: "idx_workspaces_null_config_version_id"
+    )
+  end
+end
diff --git a/db/schema_migrations/20251014140356 b/db/schema_migrations/20251014140356
new file mode 100644
index 0000000000000000000000000000000000000000..4c3f0fb96196cdf23ee0799931afd5e2b5940b07
--- /dev/null
+++ b/db/schema_migrations/20251014140356
@@ -0,0 +1 @@
+a459ee0d2bfd8f3b66a430d9411867f476832a646bd3a2459472e6075644b0fd
\ No newline at end of file
diff --git a/db/structure.sql b/db/structure.sql
index 493aecdd6d88ae010f896f299eb6a5ee3f073626..9f400f08431a18f1e0db36169897a52c87e10376 100644
--- a/db/structure.sql
+++ b/db/structure.sql
@@ -29469,7 +29469,6 @@ CREATE TABLE workspaces (
     url_prefix text,
     url_query_string text,
     workspaces_agent_config_version integer NOT NULL,
-    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)),
@@ -38386,8 +38385,6 @@ 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);