I'm on self employed package. Once ive set an invoice up and had payment into my (linked) bank account, does QB not automatically recognise payment and log?? it isn't currently

Hello Mail-mind-gap-co, Thanks for coming to the Community to ask your question! In the Self Employed package, the transactions that come through from the linked account do not impact the invoice itself. So you would have to mark the invoice as paid separately and in the banking catgorise the transaction. You can set up banking rules to auto categorise if you have regular transactions . We've included a link so you can have a look at that.