Submitting a VAT return to HMRC takes about ten minutes once your records are in order. The hard part is knowing what HMRC expects — especially since the old online form closed and every return now goes through Making Tax Digital (MTD) software. This guide walks through the whole process, box by box.
Before you start: what you need
- Your VAT registration number (VRN) — 9 digits, on your VAT certificate
- Your Government Gateway user ID and password for the business's HMRC account — you use it once to connect your software
- Your sales and purchase records for the VAT period, kept digitally
- MTD-compatible software — either full accounting software or bridging software that files figures from a spreadsheet
You can't type a VAT return into the HMRC website any more. If you logged in to HMRC expecting to find a form, here's why it isn't there.
Step 1: Check which period you're filing
Every VAT return belongs to an obligation — a period HMRC expects a return for, with a start date, an end date and a due date. Your software reads your open obligations from HMRC, so you pick the period from a list rather than typing dates.
Check the dates carefully. Your first return after registering, or after changing your VAT quarters, can be longer or shorter than three months. For due dates, see our VAT submission deadlines guide — the short version is 1 month and 7 days after the period ends.
Step 2: Get your records up to date
Before you work out any figures:
- Record every sales invoice and purchase bill dated in the period
- Reconcile your bank account so nothing is missing or doubled
- Check any credit notes, refunds and cancelled invoices
- Keep the VAT invoices that support your reclaims — HMRC can ask for them
Under MTD your records must be digital, and figures must move between spreadsheets and software through digital links, not copy and paste. If you work in Excel, see can you still file a VAT return from Excel?
Step 3: Work out the nine boxes
Every UK VAT return has the same nine boxes. Boxes 1 to 5 are VAT amounts, in pounds and pence. Boxes 6 to 9 are values excluding VAT, in whole pounds.
Box 1 — VAT due on sales and other outputs. The VAT you charged on everything you sold in the period. Include VAT you account for under the reverse charge and the domestic reverse charge.
Box 2 — VAT due on acquisitions of goods from the EU. Northern Ireland businesses only, for goods brought in from EU member states. For almost everyone else in Great Britain this is 0.
Box 3 — Total VAT due. Box 1 plus Box 2. Most software fills this in for you.
Box 4 — VAT reclaimed on purchases and other inputs. The VAT on your business purchases and expenses that you're entitled to reclaim, plus any reverse charge VAT you also put in Box 1.
Box 5 — Net VAT to pay or reclaim. The difference between Box 3 and Box 4. If Box 3 is bigger, you pay HMRC. If Box 4 is bigger, HMRC pays you.
Box 6 — Total value of sales, excluding VAT. All your sales and other outputs, including zero-rated, exempt and reverse charge sales.
Box 7 — Total value of purchases, excluding VAT. All your purchases and expenses, including zero-rated and exempt ones. Leave out wages, PAYE, NI and other items outside the scope of VAT.
Box 8 — Goods supplied to the EU. Northern Ireland only: the value of goods sold to customers in EU member states.
Box 9 — Goods acquired from the EU. Northern Ireland only: the value of goods bought from suppliers in EU member states.
If you're on the Flat Rate Scheme
Box 1 is your flat rate percentage applied to your VAT-inclusive turnover. Box 4 is normally 0, unless you're reclaiming VAT on a single capital asset costing £2,000 or more including VAT. Box 6 is your VAT-inclusive turnover.
Step 4: Connect your software to HMRC
The first time you file, your software sends you to HMRC's sign-in page. You sign in with the business's Government Gateway user ID and grant authority for the software to send VAT returns for you.
This is a one-off step. The authority lasts 18 months, after which you sign in again to renew it. You never type your HMRC password into the software itself.
Step 5: Review and submit
Before you press submit:
- Compare the figures with last quarter's — a big change usually means a missing or duplicated invoice
- Check Box 5 is the difference between Box 3 and Box 4
- Make sure Boxes 6 to 9 are in whole pounds, excluding VAT
You'll be asked to confirm a declaration that the information is true and complete. Once submitted, a return can't be withdrawn. HMRC sends back a receipt with a processing date and a form bundle number — keep it as proof you filed on time.
Made a mistake? Errors below the reporting threshold can be corrected on your next return. Larger errors are reported to HMRC separately. Don't try to file the same period twice.
Step 6: Pay HMRC (or wait for your repayment)
If Box 5 means you owe VAT, payment is due by the same deadline as the return. Use your VRN as the reference, and allow time for your payment method to clear — Bacs takes 3 working days. Our deadlines guide covers each payment method and the weekend rules.
If HMRC owes you, the repayment goes to the bank account HMRC has on record, usually within about 10 days of a correct return.
Common mistakes to avoid
- Missing the nil return. No sales this quarter? You still have to file. A late nil return earns a penalty point like any other.
- Including VAT in Boxes 6 and 7. These boxes are always excluding VAT.
- Putting wages or PAYE in Box 7. They're outside the scope of VAT.
- Reclaiming VAT without a valid VAT invoice. You need one for each reclaim.
- Reclaiming VAT on client entertaining. It isn't recoverable.
- Using the wrong period. Always file against the obligation HMRC shows, not your own idea of the quarter.
How to submit your VAT return with AccLedger
If your figures are in a spreadsheet: use our VAT bridging software. Download the nine-box Excel template, fill it in (or link it to your workings), upload it, connect to HMRC and submit. It costs £4.99 + VAT per return, with no subscription. Not sure which route suits you? Read bridging software vs full MTD VAT software.
If you want the nine boxes calculated for you: AccLedger's MTD VAT software builds the return from your invoices, bills and bank feed. It reads your open obligations from HMRC, handles the Flat Rate Scheme and Northern Ireland boxes, and submits in a few clicks.
Start a 30-day free trial — no credit card needed, and you can file your VAT returns during the trial.
Frequently asked questions
Can I submit a VAT return on the HMRC website? Not for most businesses. HMRC closed its online VAT return form for businesses that follow MTD. You need MTD-compatible software. Only businesses HMRC has exempted from MTD file another way.
How long does it take to submit a VAT return? The submission itself takes a few minutes. Getting your records ready takes longer — that's where good software saves the most time.
What is Box 5 on a VAT return? Your net VAT: the amount you pay HMRC, or the repayment HMRC owes you. It's the difference between Box 3 (VAT due) and Box 4 (VAT reclaimed).
Do I include zero-rated sales on my VAT return? Yes. Zero-rated and exempt sales go in Box 6, even though there's no VAT on them.
Can I change a VAT return after submitting it? You can't edit or withdraw a submitted return. Correct small errors on your next return, or tell HMRC about larger ones.
Can my accountant submit the VAT return for me? Yes. Accountants file through their own agent services account and software, once you've authorised them as your agent.
This article is general guidance based on HMRC rules as of October 2026 and is not tax advice. HMRC's VAT Notice 700/12 covers how to fill in each box in full.