How do I account for a GoCardless receipt due to cash being less than invoice due to fees? I need to mark invoice as paid but it's now showing £0.60 outstanding.

The difference is likely due to a processing fee deduction, meaning you will only see the net amount in your bank feed. Regardless, the invoice should automatically be coded and marked as paid in full.
 

However, because the invoice still shows an outstanding balance, it's possible it was edited after you sent the payment link. This means your customer wouldn't have seen the new total unless the link was refreshed, or they manually entered the payment amount at checkout and missed the £0.60 difference.
 

To mark your invoice as paid, please verify the exact amount received in your bank account:
 

• If the customer paid in full (and the difference is just the fee), the invoice should automatically be marked as paid.

• If the customer underpaid by £0.60 (separate from the fee), you can either ask them for the remaining balance or manually adjust the invoice to match the received payment amount.
 

You can then proceed to create a bank deposit to add the processing fee. Check this article for detailed steps: Record and make bank deposits in QuickBooks Online. Then, match it with your bank feed.
 

Please don't hesitate to drop a reply below if you have any other questions or concerns.