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Submit a VAT return in QuickBooks Online

This article is for small businesses that are not yet eligible for Making Tax Digital (MTD).
If you have signed up for MTD, go to Submit a VAT return to HMRC - MTD for small businesses.

From April 2019, all eligible UK VAT-registered businesses will have to keep their financial records in a digital form and submit their VAT returns using approved software. Find out whether you are eligible here.
If you are on the Flat Rate Scheme or submit your VAT annually and have not signed up for MTD, you will need to file through the HMRC Government Gateway. Once you have filed through the gateway, go to Mark your VAT as filed in QuickBooks to close the period.

Check your reports to make sure your figures are correct. Select the ▼ drop-down arrow next to Prepare/Submit return to view the following reports:

  • VAT 100 Report (This report shows you the summary information for each box on the VAT return.)
  • VAT Detail Report (This report lists transactions that are included in each box on the VAT return.)
  • VAT exceptions and reports (Ensure that no VAT collected, or credits earned are missed or duplicated.)

If you need to make corrections to your sales or purchase VAT, read this article to adjust your VAT liability.

To submit your VAT return directly to HMRC from Quickbooks Online, follow these steps.

  1. Go to Taxes, then select VAT
  2. Select Submit return to view your open return.
    Submit Return
  3. Confirm the dates and figures are correct. When you are ready to submit your VAT return to HMRC, select File online with HMRC.
  4. Enter your Government Gateway User ID and Government Gateway Password, then select Yes, I want to proceed. QuickBooks Online will now connect to HMRC to submit your VAT return.
  5. When HMRC receives your VAT return, you will see the "Pending with HMRC." status and a message which says "HMRC is on the case. We'll notify you when the status of your VAT return changes."
    Pending with HMRC
  1. Select Close and continue working.
  2. If your VAT submission is successful, the status will change to Approved by HMRC. You will be able to see the filing when you log into your HMRC account.Status of filed return

To review the VAT return after it has been submitted to HMRC, select the ▼ drop-down arrow against the return to view your reports. You will now see Approved by HMRC.

VAT detail report

Note: When you submit your VAT return to HMRC, QuickBooks Online creates a journal moving the amount of VAT due from the VAT Control account to the VAT Suspense

If your submission is unsuccessful, it may be for one of the following reasons:

  • Incorrect credentials (user ID or password, or both).
  • Poor internet connection causing the submission to fail or time out.
  • No information or data within the period you are trying to file.
  • Trying to submit a VAT return for a future period prior to the beginning date of when you qualified for VAT.
  • Trying to submit a VAT return before the end of your VAT period.
  • Trying to submit a VAT return after the deadline for the period.
  • Trying to submit a VAT return for incorrect dates.
  • Trying to submit a VAT return which has already been filed directly with HMRC.

If these reasons do not apply to you, please contact support.

Once you have found which reason caused HMRC to reject your VAT return, you can resubmit it.

To do this, select Resubmit return against the period.

User-added image

This will open up your return. Select Resubmit to HMRC to go through the steps above again.

User-added image

If you chose to file directly with HMRC instead, you can remove the Rejected status by selecting the arrow next to Resubmit to HMRC, then select Mark as filed.

If you don't have the option to submit your return or you prefer to file your VAT directly with HMRC, follow these steps to mark your return as filed and close the period.

  1. Go to Taxes, then select VAT.
  2. Select Prepare return to view your open return.
  3. Confirm the dates and figures are correct. When you are ready to submit your VAT return to HMRC, select File online with HMRC.
  4. Select Submit a VAT Return/Set up a VAT Direct Debit Instruction, then select Submit a return. Copy the amounts from your QuickBooks Online return to the HMRC website.
  5. Once you're done, go back to QuickBooks Online and select Mark as Filed.

Note: When you mark your VAT period as filed, QuickBooks Online creates a journal moving the amount of VAT due from the VAT Control account to the VAT Suspense.

You can now close the books to protect transactions entered in the quarter you just filed.

Once you have paid off the liability to HMRC, you can record a VAT payment or refund.

It's not possible to un-file a return that has been submitted to and approved by HMRC. QuickBooks Online follows the HMRC process that any adjustments that need to be made to a VAT return already submitted to HMRC will typically require you to make a subsequent VAT return.
For further clarification on this, we recommend contacting HMRC directly.
Not currently. However, you are able to save your HMRC user ID and password using your browser. To do this, select the prompt Remember my password, then select Save or Yes.
When typing your password, ensure you type all letters in lower case. If you are already doing this, then your VAT registration number may be causing the issue. Select Edit VAT, then select Edit settings.Make sure that there are no spaces between characters in your VAT registration number. If the number starts with GB, you will need to remove this as well.

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