Thunderbird has no automatic archiving feature. Archiving always is a manual process. https://support.mozilla.org/kb/archived-messages However, with POP you can set up your account so that all messages are left in Inbox on the server when opened with Thunderbird. Alternatively you can tell Thunderbird to remove messages from the server when opened with Thunderbird. In the latter case all you need to do is archive messages in Thunderbird, without the need to also remove them from the server.