When Thunderbird will not delete messages, the Trash folder's index database is usually corrupt. Rebuilding it from the profile folder fixes it. Jump to your situation below or work through the methods in order.
When Thunderbird refuses to delete messages, the cause is almost always a corrupt Trash folder index. Deleting a message moves it to Trash, and Thunderbird updates the Trash folder and its .msf index; if that index is damaged, the move fails and the message will not delete. The reliable fix is to rebuild the Trash: close Thunderbird, open your profile folder, and in the account's mail directory delete both the Trash file and its Trash.msf index, then reopen Thunderbird, which regenerates an empty, healthy Trash. Compacting folders and using Repair Folder on Trash are gentler first steps that often work without deleting anything. For an IMAP account, the issue can instead be that the Trash folder is not mapped correctly or the server mailbox is over quota, which is worth checking too.
Deleting a message in Thunderbird does not erase it immediately, it moves it to the Trash folder. Thunderbird then updates the Trash folder file and its .msf index. If that update cannot complete, the original message will not leave its folder, so it looks like delete is broken.
The thing that usually cannot complete is the index. The .msf file that tracks the Trash contents gets corrupt, and Thunderbird cannot write the moved message into it. Because the index is rebuilt automatically, removing the Trash and its index lets Thunderbird create a clean one and deleting works again.
“If delete just does nothing, it is the Trash that is broken, not the message. Thunderbird moves deletions into Trash and updates its index, and when that index rots the move fails silently. The clean fix is to close Thunderbird, go into the profile, and delete the Trash file and its Trash.msf, then reopen, Thunderbird builds a fresh empty Trash and deleting works instantly. Try Compact and Repair Folder first, they are gentler and often enough on their own.”
Trash and Trash.msf.A delete that does nothing is a Trash-index problem, not a problem with the message. Try Compact and Repair Folder on Trash first, since they are gentle and often enough. If they do not work, closing Thunderbird and deleting the Trash and Trash.msf files lets Thunderbird build a clean Trash and restores deleting.
If rebuilding Trash does not help and deletion still fails across folders, the profile may have wider index corruption or a permissions problem. Repair each affected folder, check that your account can write to the profile directory, and as a last resort create a new profile and migrate your accounts. You can also submit your error to us for a tailored fix.