diff --git a/redbot/cogs/cleanup/cleanup.py b/redbot/cogs/cleanup/cleanup.py
index 8c61dc172..5b941f3c5 100644
--- a/redbot/cogs/cleanup/cleanup.py
+++ b/redbot/cogs/cleanup/cleanup.py
@@ -1,6 +1,6 @@
 import re
 from datetime import datetime, timedelta
-from typing import Union, List, Callable
+from typing import Union, List, Callable, Set
 
 import discord
 
@@ -323,15 +323,35 @@ class Cleanup(commands.Cog):
         if "" in prefixes:
             prefixes.remove("")
 
+        cc_cog = self.bot.get_cog("CustomCommands")
+        if cc_cog is not None:
+            command_names: Set[str] = await cc_cog.get_command_names(ctx.guild)
+            is_cc = lambda name: name in command_names
+        else:
+            is_cc = lambda name: False
+        alias_cog = self.bot.get_cog("Alias")
+        if alias_cog is not None:
+            alias_names: Set[str] = (
+                set((a.name for a in await alias_cog.unloaded_global_aliases()))
+                | set(a.name for a in await alias_cog.unloaded_aliases(ctx.guild))
+            )
+            is_alias = lambda name: name in alias_names
+        else:
+            is_alias = lambda name: False
+
+        bot_id = self.bot.user.id
+
         def check(m):
-            if m.author.id == self.bot.user.id:
+            if m.author.id == bot_id:
                 return True
             elif m == ctx.message:
                 return True
             p = discord.utils.find(m.content.startswith, prefixes)
             if p and len(p) > 0:
                 cmd_name = m.content[len(p) :].split(" ")[0]
-                return bool(self.bot.get_command(cmd_name))
+                return (
+                    bool(self.bot.get_command(cmd_name)) or is_alias(cmd_name) or is_cc(cmd_name)
+                )
             return False
 
         to_delete = await self.get_messages_for_deletion(
diff --git a/redbot/cogs/customcom/customcom.py b/redbot/cogs/customcom/customcom.py
index 095755de2..acaa9164e 100644
--- a/redbot/cogs/customcom/customcom.py
+++ b/redbot/cogs/customcom/customcom.py
@@ -3,7 +3,7 @@ import random
 from datetime import datetime, timedelta
 from inspect import Parameter
 from collections import OrderedDict
-from typing import Mapping, Tuple, Dict
+from typing import Mapping, Tuple, Dict, Set
 
 import discord
 
@@ -553,3 +553,14 @@ class CustomCommands(commands.Cog):
         else:
             return raw_result
         return str(getattr(first, second, raw_result))
+
+    async def get_command_names(self, guild: discord.Guild) -> Set[str]:
+        """Get all custom command names in a guild.
+
+        Returns
+        --------
+        Set[str]
+            A set of all custom command names.
+
+        """
+        return set(await CommandObj.get_commands(self.config.guild(guild)))