Glad to see you in the Community, @usmanrauf. I’ll make sure this will resolve to keep your books balanced.
Since the Vat return is already submitted, I recommend contacting our support team to correct this. They can help handle this situation to ensure all linked transactions with this return are accurate. Here’s how:
- Open your QuickBooks Online account.
- Select Help (?).
- Go to the Search tab, then select Contact Us.
- Enter a brief description of concern in the box.
- Choose a way to connect with us:
- Start a chat with a support expert (Live chat all day, Monday-Friday)
- Get a callback (Monday-Friday) 8:00 AM to 10:00 PM and Saturday-Sunday, 8:00 AM to 6:00 PM)
If you receive a VAT refund from HMRC for the overpayment, you can track it in the program. This way, you can make a match with the associated bank transaction. I’m glad to show you the steps:
- Go to the Taxes menu.
- Click VAT.
- Click the All returns dropdown menu, then choose the specific VAT period you need.
- Choose Record Refund in the View summary/return dropdown menu.
- Select the bank account the refund has gone into.
- Make sure you've selected Refund under Payment Type.
- Enter the refund date and amount in the appropriate fields.
- Add a memo if needed.
- Tap Save after.

In case you want to make adjustments to your VAT due and liability moving forward, you can bookmark these articles for complete instructions:
I'm just around if you have any other concerns or questions besides your VAT returns. Just add them to your reply below, and I'll get back to you as soon as I can. Keep safe always!