I am coming at this at a bit of a loss, as I am not aware of any new gmail integration. There have been a few incremental changes over the years, but the only real change I have seen is in contact synchronization and even that was available in an add-on prior to Thunderbird's own implementation. So if I am missing something obvious sorry. Gmail only has one message store (the all mail folder), and lots of labels which it presents as folders under IMAP. Thunderbird has as of now a more historical IMAP approach of a mail store per folder (it is the standard for IMAP servers, only google is out there with a single global store and Microsoft with a completely proprietary process with standards glued on as an after thought) The upshot is Thunderbird has two emails, where Gmail has only one linked to a global store so there is no real way to emulate the gmail flow in Thunderbird. I understand a global message store is under consideration or development, but that does nothing for now. For now you should remove the inbox label from the emails on gmail when they are archived and Thunderbird will not have them delivered to the inbox by gmail. At least under IMAP. POP is not really suitable for trying to do more than download all mail delivered to an account. Note that gmail archiving is removing all labels from the message and it remains in the All mail folder. Thunderbird does essentially the same thing with it's archiving of gmail and local settings to the contrary are ignored, except that the archiving is done on a per folder basis not per email basis so archiving one copy does not get all instances of the email.