diff --git a/src/google/adk/cli/cli_tools_click.py b/src/google/adk/cli/cli_tools_click.py
index 07ccc15892..a41de4ef72 100644
--- a/src/google/adk/cli/cli_tools_click.py
+++ b/src/google/adk/cli/cli_tools_click.py
@@ -1632,8 +1632,12 @@ def cli_web(
 ):
   """Starts a FastAPI server with Web UI for agents.
 
-  AGENTS_DIR: The directory of agents, where each subdirectory is a single
-  agent, containing at least `__init__.py` and `agent.py` files.
+  AGENTS_DIR: The directory of agents. Each subdirectory (or file) can contain an agent
+  loaded via multiple formats:
+    - `{agent_name}/agent.py` (module with `root_agent`)
+    - `{agent_name}.py` (module with `root_agent`)
+    - `{agent_name}/__init__.py` (package with `root_agent` or `app`)
+    - `{agent_name}/root_agent.yaml` (YAML config folder)
 
   Example:
 
@@ -1745,8 +1749,12 @@ def cli_api_server(
 ):
   """Starts a FastAPI server for agents.
 
-  AGENTS_DIR: The directory of agents, where each subdirectory is a single
-  agent, containing at least `__init__.py` and `agent.py` files.
+  AGENTS_DIR: The directory of agents. Each subdirectory (or file) can contain an agent
+  loaded via multiple formats:
+    - `{agent_name}/agent.py` (module with `root_agent`)
+    - `{agent_name}.py` (module with `root_agent`)
+    - `{agent_name}/__init__.py` (package with `root_agent` or `app`)
+    - `{agent_name}/root_agent.yaml` (YAML config folder)
 
   Example:
 
diff --git a/src/google/adk/runners.py b/src/google/adk/runners.py
index 8e352794a4..75833f83c5 100644
--- a/src/google/adk/runners.py
+++ b/src/google/adk/runners.py
@@ -825,12 +825,26 @@ async def _exec_with_plugin(
       _apply_run_config_custom_metadata(
           early_exit_event, invocation_context.run_config
       )
-      if self._should_append_event(early_exit_event, is_live_call):
+      # Step 3: Run the on_event callbacks to optionally modify the event.
+      # This MUST run before append_event so modifications are persisted.
+      modified_early_exit_event = await plugin_manager.run_on_event_callback(
+          invocation_context=invocation_context, event=early_exit_event
+      )
+      if modified_early_exit_event:
+        _apply_run_config_custom_metadata(
+            modified_early_exit_event, invocation_context.run_config
+        )
+        event_to_append = modified_early_exit_event
+      else:
+        event_to_append = early_exit_event
+      # Step 4: Append the (possibly modified) event to the database.
+      if self._should_append_event(event_to_append, is_live_call):
         await self.session_service.append_event(
             session=session,
-            event=early_exit_event,
+            event=event_to_append,
         )
-      yield early_exit_event
+      # Step 5: Yield the modified event to the client.
+      yield modified_early_exit_event if modified_early_exit_event else early_exit_event
     else:
       # Step 2: Otherwise continue with normal execution
       # Note for live/bidi:
@@ -868,6 +882,17 @@ async def _exec_with_plugin(
             # non-partial event; event.partial=True is considered as partial
             # event.
             if event.partial is not True:
+              # Step 3: Run the on_event callbacks to optionally modify the event.
+              # This MUST run before append_event so modifications are persisted.
+              modified_event = await plugin_manager.run_on_event_callback(
+                  invocation_context=invocation_context, event=event
+              )
+              if modified_event:
+                _apply_run_config_custom_metadata(
+                    modified_event, invocation_context.run_config
+                )
+                event = modified_event  # Use modified event for appending
+
               if _is_transcription(event) and (
                   _has_non_empty_transcription_text(event.input_transcription)
                   or _has_non_empty_transcription_text(
@@ -899,22 +924,25 @@ async def _exec_with_plugin(
                   await self.session_service.append_event(
                       session=session, event=event
                   )
+            # Step 5: Yield the event to the caller.
+            yield event
           else:
+            # Step 3: Run the on_event callbacks to optionally modify the event.
+            # This MUST run before append_event so modifications are persisted.
+            modified_event = await plugin_manager.run_on_event_callback(
+                invocation_context=invocation_context, event=event
+            )
+            if modified_event:
+              _apply_run_config_custom_metadata(
+                  modified_event, invocation_context.run_config
+              )
+              event = modified_event  # Use modified event for appending and yielding
+            # Step 4: Append the event to the database (after on_event_callback).
             if event.partial is not True:
               await self.session_service.append_event(
                   session=session, event=event
               )
-
-          # Step 3: Run the on_event callbacks to optionally modify the event.
-          modified_event = await plugin_manager.run_on_event_callback(
-              invocation_context=invocation_context, event=event
-          )
-          if modified_event:
-            _apply_run_config_custom_metadata(
-                modified_event, invocation_context.run_config
-            )
-            yield modified_event
-          else:
+            # Step 5: Yield the event to the caller.
             yield event
 
     # Step 4: Run the after_run callbacks to perform global cleanup tasks or