GoCradless

I recommend reaching out to our Live Support team for a deeper look. They have specialized tools to determine the root cause of the syncing issue and follow the next guided steps.

Just head over to the Help (?) icon in the upper right of your screen. From the Search tab, select the Contact Us button below. Enter the problem in the box, then click Continue. Choose Callback. To learn about our support hours, feel free to visit this resource: How to get help with QuickBooks. 

For now, we can manually mark the QBO invoices as paid since the payment has already been processed/received through your GoCardless or your bank account by navigating to the + Create in your QuickBooks Online. Choose Receive payment, then select the Customer, Payment method, and account you put the payment from the Deposit to dropdown. Hit Save once done.

You can add a Reply below if you have any follow-up questions or any other concerns about QuickBooks. We're here to help.        

I think it is a known issue with Intuit and GoCardless (Intuit didn't implement the longer key number format or something), see below forum topic.  

Gocardless Deposits not being created since 24/04/26