After making a joint payment of gst and payg to the ato, i recorded the gst amount being paid and the money has come out of the account again in Chart of Accounts

Hi murrayderrick6,

Thanks for posting in the Community! If you've lodged your BAS in QuickBooks Online GST centre, this automatically creates a journal to your ATO Clearing account. Firstly, you record the payment in the GST centre by clicking on Record payment, then you match this to the BAS payment in your bank feed. Here's how to match the GST payment recorded to your bank feed.

1. Go to Banking tab.
2. Select the GST payment downloaded.
3. The bank feeds usually recognize the math if the date and amount are the same and correct.
4. Click on Match.
5. If you don't see Match automatically, click on Find Match to see the transactions.

If you've added the bank feed without matching it to the payment you've manually recorded in QuickBooks Online, this will cause duplicate. You can undo the transaction by going to Categorised tab and select Undo. This transaction will be moved to the For Review tab where you can then match it to your GST payment.

For your reference, you can check on this article: Recording a GST payment (BAS Payment) in QuickBooks Online.

Feel free to drop a comment below if you need further assistance. Have a great day!