Thunderbird: Purge Deleted Mail
If you are here because you are at or over your mail quota, you must actually remove (purge, expunge) deleted mail to free space used by that mail. Proceed directly to Where Deleted Mail Is Now.
If you are here because you are close to or at your quota, change the Thunderbird setting to "Remove it immediately" as described in "Setting How to Handle Deleted Mail" below.
If you are here because you want to know in advance how to really remove mail, read at your leisure.
You can delete a message in several ways whether or not you are viewing the message. Highlight or open the message and: 1) click the Delete icon in the Toolbar, 2) press the Delete key, or 3) select Edit | Delete Message.
The default setting for Thunderbird is to put deleted messages in the Trash. Messages moved to the Trash folder are deleted after being in the Trash for 7 days. You can immediately regain space by compacting folders, File | Compact Folders. Your mail quota reflects that difference.
Setting How to Handle Deleted Mail
To change how deleted mail is handled, go to Tools | Account Settings | Server Settings. "When I delete a message" is set by default to Move it to the Trash Folder. Change that setting to "Remove it immediately" or "Mark it as deleted." If remove immediately is set, the message will not go to the Trash folder. If mark as deleted is set, deleted messages show a line through the text and an icon of a red "X".
Also set Clean up ("Expunge") Inbox on Exit so messages get deleted when you exit from Thunderbird.