The message you receive is from the server not Thunderbird. If you right click on the eg: inbox folder and select 'compact' this should remove traces of deleted emails. to compact a folder: right click on a folder and select 'compact' to compact all folders: File > Compact folders If this is an IMAP mail account, did you set it up the auto expunge? Tools -> Account Settings -> Server Settings for the imap mail account select: Clean up ("Expunge") Inbox on Exit this will compact the Inbox folder when you exit Thunderbird. If you check "Empty Trash on Exit" it will also empty and compact the Trash folder when you exit. If this is a POP mail account do you leave a copy on the server? Tools -> Account Settings -> Server Settings for the imap mail account select: Leave messages on server If yes, you have that setting and you want this to remain, then you could use the additional options to delete off server after xx daysor when you delete them. I would also logon to webmail to check what is on server.