When using go cardless I have found that on a couple of occasions the automatically entered customer payment has not adjusted for the fee deducted how do I adjust?

It's nice to see you here in the Community, Linda Fowler.

Deducting the fee for the customer's payment is quick and easy. You can create a bank deposit for the payment and enter the fee as negative amount.

Here's how:

1. Click the + New in the left panel and choose Bank deposits.
2. Select the customer's payment.
3. In the Add funds to this deposit field, choose the relevant account.
4. Enter a negative amount, under Amount.
5. Click Save and close.

To help you manage your fees in QuickBooks, see these articles:

GoCardless Welcome Guide

Add service fees manually to invoices

Let me know if there's anything else you need with recording your fees in QuickBooks, I'll be around to help. You have a wonderful day!