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Record VAT-only and CIS transactions in QuickBooks

by Intuit•15• Updated 2 weeks ago

There may be times when you need to record a transaction that includes VAT only or log a CIS payment to HMRC. Learn how to do both accurately, so your VAT returns and reports stay up to date.

This article is for customers who use QuickBooks Online.

Record a VAT-only or 100% VAT transaction

You can record a VAT-only transaction using an expense or by adjusting your VAT return directly. Choose the method that best suits your reporting and reconciliation needs.

Use this method if you want the transaction to show in your supplier list, reports, and bank feed.

  1. Select + New, then choose Expense.
  2. Select a payee, or leave it blank if not needed.

On the first line:

  • Choose any Expense account.
  • In the Amount field, enter the VAT exclusive amount (e.g. 1,500).
  • Select 20.0% S as the VAT code.

On the second line:

  • Enter the same amount as a negative (e.g. -1,500).
  • Select Exempt as the VAT code.
  1. The total should now be £0, with VAT appearing in the VAT section.
  2. If needed, manually edit the VAT box to reflect the correct amount.
  3. Save the expense.

This will create a VAT-only transaction that appears in Box 4 of your VAT return.

If you only need to adjust the VAT return and don’t need a corresponding supplier or bank transaction, use this method.

  1. Go to Taxes, select VAT, then choose Prepare return.
  2. Next to Box 1 or Box 4, select Adjust.
  3. Enter the date of the transaction.
  4. Choose the relevant VAT code and the account used for the adjustment.
  5. Enter the amount.
  6. Add a memo or note for reference.
  7. Select Save.

Important notes:

  • This method does not create a supplier transaction.
  • It will not match to your bank feed – you’ll need to manually exclude and reconcile any related transaction.
  • The adjustment won’t appear in the supplier list. To find or delete it later, go to the account history or use a report.

Record a CIS payment made to HMRC

After submitting your CIS return, it’s important to record the payment made to HMRC. This ensures your CIS reports and bank feed stay accurate and aligned.

  1. Select + New, then choose Expense.
  2. In the Payee field, enter HMRC (if you’ve set them up as a supplier).
  3. Choose the bank account and payment method.
  4. Set the payment date.
  5. Under the Category column, select CIS Payments to HMRC.
  6. Enter the amount paid.
  7. Select Save and close.

Tip: Match your bank transactions before running CIS reports to ensure everything lines up.

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