Right click on mail account in Folder Pane and select 'Settings' select 'Server Settings' Under Message Storage select checkbox 'Empty deleted Folder on exit' If this is an imap mail account you coulc also select to 'Clean up (Expunge) Inbox on exit.' in same location. click on OK Then all is cleared when you exit Thunderbird. To manually delete all messages in Deleted/Trash folder; Right click on folder and select 'Empty Deleted' Note: some imap accounts will auto empty the imap Trash folder after a period of eg: 30 days.