diff --git a/discord/ext/commands/cog.py b/discord/ext/commands/cog.py
index 0e35021a1..3ca0b7731 100644
--- a/discord/ext/commands/cog.py
+++ b/discord/ext/commands/cog.py
@@ -305,6 +305,7 @@ class Cog(metaclass=CogMeta):
 
         # Register the application commands
         children: List[Union[app_commands.Group, app_commands.Command[Self, ..., Any]]] = []
+        app_command_refs: Dict[str, Union[app_commands.Group, app_commands.Command[Self, ..., Any]]] = {}
 
         if cls.__cog_is_app_commands_group__:
             group = app_commands.Group(
@@ -331,6 +332,16 @@ class Cog(metaclass=CogMeta):
                 # Get the latest parent reference
                 parent = lookup[parent.qualified_name]  # type: ignore
 
+                # Hybrid commands already deal with updating the reference
+                # Due to the copy below, so we need to handle them specially
+                if hasattr(parent, '__commands_is_hybrid__') and hasattr(command, '__commands_is_hybrid__'):
+                    app_command: Optional[Union[app_commands.Group, app_commands.Command[Self, ..., Any]]] = getattr(
+                        command, 'app_command', None
+                    )
+                    updated = app_command_refs.get(command.qualified_name)
+                    if app_command and updated:
+                        command.app_command = updated  # type: ignore  # Safe attribute access
+
                 # Update our parent's reference to our self
                 parent.remove_command(command.name)  # type: ignore
                 parent.add_command(command)  # type: ignore
@@ -345,6 +356,11 @@ class Cog(metaclass=CogMeta):
                     # The type checker does not see the app_command attribute even though it exists
                     command.app_command = app_command  # type: ignore
 
+                    # Update all the references to point to the new copy
+                    if isinstance(app_command, app_commands.Group):
+                        for child in app_command.walk_commands():
+                            app_command_refs[child.qualified_name] = child
+
                     if self.__cog_app_commands_group__:
                         children.append(app_command)  # type: ignore # Somehow it thinks it can be None here
 
diff --git a/tests/test_app_commands_group.py b/tests/test_app_commands_group.py
index d5f07976f..228debde6 100644
--- a/tests/test_app_commands_group.py
+++ b/tests/test_app_commands_group.py
@@ -397,3 +397,85 @@ def test_cog_group_with_custom_state_issue9383():
     assert cog.inner.my_command.parent is cog.inner
     assert cog.my_inner_command.parent is cog.inner
     assert cog.my_inner_command.binding is cog
+
+
+def test_cog_hybrid_group_manual_command():
+    class MyCog(commands.Cog):
+        @commands.hybrid_group()
+        async def first(self, ctx: commands.Context) -> None:
+            ...
+
+        @first.command(name='both')
+        async def second_both(self, ctx: commands.Context) -> None:
+            ...
+
+        @first.app_command.command(name='second')
+        async def second_app(self, interaction: discord.Interaction) -> None:
+            ...
+
+    client = discord.Client(intents=discord.Intents.default())
+    tree = app_commands.CommandTree(client)
+
+    cog = MyCog()
+    tree.add_command(cog.first.app_command)
+
+    assert cog.first is not MyCog.first
+    assert cog.second_both is not MyCog.second_both
+    assert cog.second_app is not MyCog.second_app
+    assert cog.first.parent is None
+    assert cog.second_both.parent is cog.first
+    assert cog.second_app.parent is cog.first.app_command
+    assert cog.second_app.binding is cog
+    assert tree.get_command('first') is cog.first.app_command
+
+    first = tree.get_command('first')
+    assert isinstance(first, app_commands.Group)
+    both = first.get_command('both')
+    assert isinstance(both, app_commands.Command)
+    assert both.parent is first
+    assert both.binding is cog
+
+    second = first.get_command('second')
+    assert isinstance(second, app_commands.Command)
+    assert second.parent is first
+    assert second.binding is cog
+
+
+def test_cog_hybrid_group_manual_nested_command():
+    class MyCog(commands.Cog):
+        @commands.hybrid_group()
+        async def first(self, ctx: commands.Context) -> None:
+            pass
+
+        @first.group()
+        async def second(self, ctx: commands.Context) -> None:
+            pass
+
+        @second.app_command.command()
+        async def third(self, interaction: discord.Interaction) -> None:
+            pass
+
+    client = discord.Client(intents=discord.Intents.default())
+    tree = app_commands.CommandTree(client)
+
+    cog = MyCog()
+    tree.add_command(cog.first.app_command)
+
+    assert cog.first is not MyCog.first
+    assert cog.second is not MyCog.second
+    assert cog.third is not MyCog.third
+    assert cog.first.parent is None
+    assert cog.second.parent is cog.first
+    assert cog.third.parent is cog.second.app_command
+    assert cog.third.binding is cog
+
+    first = tree.get_command('first')
+    assert isinstance(first, app_commands.Group)
+
+    second = first.get_command('second')
+    assert isinstance(second, app_commands.Group)
+
+    third = second.get_command('third')
+    assert isinstance(third, app_commands.Command)
+    assert third.parent is second
+    assert third.binding is cog