diff --git a/api/controllers/console/app/model_config.py b/api/controllers/console/app/model_config.py
index e71b774d3e..fa6e3f8738 100644
--- a/api/controllers/console/app/model_config.py
+++ b/api/controllers/console/app/model_config.py
@@ -14,6 +14,7 @@ from core.tools.tool_manager import ToolManager
 from core.tools.utils.configuration import ToolParameterConfigurationManager
 from events.app_event import app_model_config_was_updated
 from extensions.ext_database import db
+from libs.datetime_utils import naive_utc_now
 from libs.login import login_required
 from models.account import Account
 from models.model import AppMode, AppModelConfig
@@ -172,6 +173,8 @@ class ModelConfigResource(Resource):
         db.session.flush()
 
         app_model.app_model_config_id = new_app_model_config.id
+        app_model.updated_by = current_user.id
+        app_model.updated_at = naive_utc_now()
         db.session.commit()
 
         app_model_config_was_updated.send(app_model, app_model_config=new_app_model_config)
diff --git a/api/controllers/console/app/workflow.py b/api/controllers/console/app/workflow.py
index 1f5cbbeca5..578d864b80 100644
--- a/api/controllers/console/app/workflow.py
+++ b/api/controllers/console/app/workflow.py
@@ -25,6 +25,7 @@ from factories import file_factory, variable_factory
 from fields.workflow_fields import workflow_fields, workflow_pagination_fields
 from fields.workflow_run_fields import workflow_run_node_execution_fields
 from libs import helper
+from libs.datetime_utils import naive_utc_now
 from libs.helper import TimestampField, uuid_value
 from libs.login import current_user, login_required
 from models import App
@@ -674,8 +675,12 @@ class PublishedWorkflowApi(Resource):
                 marked_comment=args.marked_comment or "",
             )
 
-            app_model.workflow_id = workflow.id
-            db.session.commit()  # NOTE: this is necessary for update app_model.workflow_id
+            # Update app_model within the same session to ensure atomicity
+            app_model_in_session = session.get(App, app_model.id)
+            if app_model_in_session:
+                app_model_in_session.workflow_id = workflow.id
+                app_model_in_session.updated_by = current_user.id
+                app_model_in_session.updated_at = naive_utc_now()
 
             workflow_created_at = TimestampField().format(workflow.created_at)
 
diff --git a/api/services/app_dsl_service.py b/api/services/app_dsl_service.py
index 311f80bef6..e2915ebfbb 100644
--- a/api/services/app_dsl_service.py
+++ b/api/services/app_dsl_service.py
@@ -29,6 +29,7 @@ from core.workflow.nodes.tool.entities import ToolNodeData
 from events.app_event import app_model_config_was_updated, app_was_created
 from extensions.ext_redis import redis_client
 from factories import variable_factory
+from libs.datetime_utils import naive_utc_now
 from models import Account, App, AppMode
 from models.model import AppModelConfig
 from models.workflow import Workflow
@@ -439,6 +440,7 @@ class AppDslService:
             app.icon = icon
             app.icon_background = icon_background or app_data.get("icon_background", app.icon_background)
             app.updated_by = account.id
+            app.updated_at = naive_utc_now()
         else:
             if account.current_tenant_id is None:
                 raise ValueError("Current tenant is not set")