diff --git a/ee/lib/tasks/gitlab/duo_workflow/duo_workflow.rake b/ee/lib/tasks/gitlab/duo_workflow/duo_workflow.rake
index 957d000f72bae99835b08d1b89e7c10cfa96e7dd..b6995c5287d8bb52707b2a9b4584f6344839f458 100644
--- a/ee/lib/tasks/gitlab/duo_workflow/duo_workflow.rake
+++ b/ee/lib/tasks/gitlab/duo_workflow/duo_workflow.rake
@@ -30,7 +30,7 @@ namespace :gitlab do
       raise 'This task cannot be run in production' if Rails.env.production?
 
       # rubocop:disable Rake/TopLevelMethodDefinition -- Instance metods withing task scope do not leak
-      def create_checkpoint_data(workflow_goal, workflow_status, step = 0)
+      def create_checkpoint_data(workflow_goal, workflow_status, step = 0, previous_checkpoint_thread_ts = nil)
         # rubocop:enable Rake/TopLevelMethodDefinition
         timestamp = Time.current.iso8601(6)
 
@@ -132,7 +132,7 @@ namespace :gitlab do
         }
 
         {
-          parent_ts: step > 0 ? Gitlab::Utils.uuid_v7 : nil,
+          parent_ts: step > 0 ? previous_checkpoint_thread_ts : nil,
           thread_ts: Gitlab::Utils.uuid_v7,
           checkpoint: checkpoint_data,
           metadata: metadata
@@ -401,8 +401,9 @@ namespace :gitlab do
                              end
 
         # Create workflow checkpoints
+        previous_thread_ts = nil
         checkpoint_configs.each_with_index do |config, checkpoint_index|
-          checkpoint_data = create_checkpoint_data(goal, config[:workflow_status], checkpoint_index)
+          checkpoint_data = create_checkpoint_data(goal, config[:workflow_status], checkpoint_index, previous_thread_ts)
 
           Ai::DuoWorkflows::Checkpoint.create!(
             workflow: workflow,
@@ -413,6 +414,8 @@ namespace :gitlab do
             metadata: checkpoint_data[:metadata]
           )
 
+          # Store the current thread_ts for the next checkpoint's parent_ts
+          previous_thread_ts = checkpoint_data[:thread_ts]
           checkpoints_created += 1
         end
 
diff --git a/ee/spec/tasks/gitlab/duo_workflow/duo_workflow_spec.rb b/ee/spec/tasks/gitlab/duo_workflow/duo_workflow_spec.rb
index 0cedd6981b7a4dee34769041d6938b2eb72d3013..1416672d39603ad21db22f4674a631cd67011c8e 100644
--- a/ee/spec/tasks/gitlab/duo_workflow/duo_workflow_spec.rb
+++ b/ee/spec/tasks/gitlab/duo_workflow/duo_workflow_spec.rb
@@ -185,6 +185,42 @@
         expect(first_message).to include('Starting workflow with goal:')
         expect(first_message).to include(workflow.goal.split(' (Workflow #').first)
       end
+
+      it 'creates checkpoints with correct parent_ts relationships' do
+        run_rake_task('gitlab:duo_workflow:populate', '5', '2')
+
+        workflows = Ai::DuoWorkflows::Workflow.all
+        workflows.each do |workflow|
+          checkpoints = workflow.checkpoints.order(:created_at)
+
+          # First checkpoint should have nil parent_ts
+          expect(checkpoints.first.parent_ts).to be_nil
+
+          # Subsequent checkpoints should have parent_ts referencing the previous checkpoint's thread_ts
+          if checkpoints.count > 1
+            checkpoints[1..-1].each_with_index do |checkpoint, index|
+              previous_checkpoint = checkpoints[index]
+              expect(checkpoint.parent_ts).to eq(previous_checkpoint.thread_ts)
+            end
+          end
+        end
+      end
+
+      it 'ensures parent_ts references actual existing checkpoint thread_ts values' do
+        run_rake_task('gitlab:duo_workflow:populate', '3', '1')
+
+        workflows = Ai::DuoWorkflows::Workflow.all
+        all_thread_ts_values = Ai::DuoWorkflows::Checkpoint.pluck(:thread_ts)
+
+        workflows.each do |workflow|
+          workflow.checkpoints.each do |checkpoint|
+            if checkpoint.parent_ts.present?
+              # parent_ts should reference an existing thread_ts
+              expect(all_thread_ts_values).to include(checkpoint.parent_ts)
+            end
+          end
+        end
+      end
     end
 
     it 'uses default values when no arguments provided' do