Fixing errors in Making Tax Digital for Income Tax in QuickBooks

Learn how to correct mistakes in your Making Tax Digital for Income Tax records — whether you spot them before your next quarterly update or after you've submitted your Final Declaration.

Transitioning to quarterly reporting with Making Tax Digital for Income Tax (MTD for IT) is a big change. It's normal to have questions about accuracy, or about what to do when you realise something is missing.

The good news is that MTD for IT is designed to be flexible. Most errors can be corrected without resubmitting anything, and figures you've already filed can be amended within HMRC's time limits. This guide covers the common issues and how to resolve each one.

I missed an expense from a previous quarter

If you find a receipt or invoice that should have been included in a quarter you've already submitted, you don't need to re-open or resubmit that quarter.

The solution: add the transaction to QuickBooks with its correct date.

How it works: MTD updates in QuickBooks are submitted as cumulative year-to-date figures, so the missing amount is picked up automatically and included in your next quarterly update — provided you're still in the same tax year.

If the tax year has already closed and you've submitted your Final Declaration, you can still put it right. See the Amending figures you've already filed section below.

Something is missing from my summary, like CIS deductions

If you're a subcontractor under the Construction Industry Scheme (CIS), you might notice your deductions aren't showing in your quarterly summaries.

The reason: quarterly updates focus on your gross income and allowable expenses.

The solution: CIS deductions suffered aren't part of the quarterly summary. You review and claim these credits during the Final Declaration at the end of the year, to reduce your final tax bill.

How do I handle a 31 March year end?

If your accounting year ends on 31 March rather than 5 April, your accounting period and the tax year don't line up exactly — there's a short gap between 1 and 5 April.

You don't need to account for those days separately in your quarterly updates. HMRC lets you treat a period ending on 31 March as though it ended on 5 April — you make this adjustment when you complete your annual tax return (Final Declaration), not during your quarterly submissions.

I categorised a transaction incorrectly

If you submitted an update and later realised a Travel expense should have been Office supplies, you can fix it.

1. Find the transaction in your Expenses or Banking tab.
2. Change the category to the correct one.

QuickBooks records the change. When you prepare your next quarterly update, your year-to-date totals reflect the corrected categories, so HMRC has the right data by the end of the year.

Amending figures you've already filed

Submitting a quarterly update or a Final Declaration doesn't lock your figures permanently. You can amend what you've filed within the time limits HMRC allows.

Before your Final Declaration: Corrections to any quarter in the current tax year are handled automatically. Because updates are cumulative, you change the transaction in QuickBooks and the next update carries the corrected year-to-date position. There's nothing separate to submit.

After your Final Declaration: Once you've submitted your Final Declaration for a tax year, that's your formal statement of income for the year — but it can still be amended within HMRC's allowed time limits if you later find something wrong.

I'm seeing a submission error

If you see an error message when trying to submit, check these three things.

1. 403 Forbidden. Your digital handshake with HMRC has expired. Go to your Income Tax settings and select Re-authorise. HMRC authorisations last 18 months, so this happens periodically even when nothing else has changed. For more on granting authority, see Set up Making Tax Digital for Income Tax.
2. Pending status. HMRC's servers can be slow at peak times. A pending update is usually still processing — wait for your confirmation before resubmitting, because submitting twice can create duplicate figures.
3. Individual is not mandated. This usually means you haven't completed the sign-up process on the HMRC website, even if you already have a Government Gateway ID.

I missed a submission deadline

HMRC uses a points-based penalty system rather than issuing a fine for every missed deadline.

Points, not immediate fines. If you miss a deadline, you typically receive one penalty point. A financial penalty applies only once you reach HMRC's points threshold. For current thresholds and amounts, see HMRC's Late submission penalties guidance.

HMRC currently operates a soft landing and won't apply late-submission penalty points for the first four quarterly updates (April 2026 – April 2027).

Tips for keeping your records accurate

• Nil updates:  If you had no business activity for three months, you still need to submit a nil update to tell HMRC you're compliant.
• Mapping questions: Use the Preview tax mapping feature in the Income Tax centre to see which HMRC box each of your QuickBooks categories is assigned to.
• Digital links: Never fix an error by copying, pasting, or manually typing into an HMRC portal. Always make the change inside QuickBooks so your digital link stays unbroken.

More help

• Making Tax Digital for Income Tax Resource Hub
• Set up Making Tax Digital for Income Tax
• MTD for IT: Accountant FAQs in QuickBooks