Filing VAT Returns via MTD

Key facts

Under MTD for VAT, you file your VAT return through MTD-compatible software, not the HMRC online portal.
The return contains the same nine boxes as before — MTD does not change what you report, only how.
Your software submits the return to HMRC via secure APIs and receives an acknowledgement.
You must still meet the normal VAT return deadlines — typically one calendar month and seven days after the end of your VAT period.
GoFile is HMRC-recognised for MTD VAT filing — try it free.

Filing VAT Returns Under MTD

Under Making Tax Digital for VAT, you submit your VAT return to HMRC through MTD-compatible software. The return itself has not changed — it still contains the same nine boxes — but the method of submission has moved from the HMRC online portal to direct software-to-HMRC filing via APIs.^[1]

The Nine-Box VAT Return

The VAT return under MTD contains the same nine boxes as the traditional return:^[3]

Box	Description
Box 1	VAT due on sales and other outputs
Box 2	VAT due on acquisitions from other EU member states (legacy — typically £0 post-Brexit)
Box 3	Total VAT due (Box 1 + Box 2)
Box 4	VAT reclaimed on purchases and other inputs
Box 5	Net VAT to pay or reclaim (Box 3 − Box 4)
Box 6	Total value of sales (excluding VAT)
Box 7	Total value of purchases (excluding VAT)
Box 8	Total value of supplies to EU member states (excluding VAT)
Box 9	Total value of acquisitions from EU member states (excluding VAT)

Your software calculates these figures from your digital records and presents them for your review before submission. GoFile’s VAT filing software does this automatically from a spreadsheet import or manual entry.

Step-by-Step: Filing Your MTD VAT Return

Step 1: Maintain Digital Records

Throughout your VAT period, record all sales and purchase transactions in your MTD-compatible software. Each transaction should include the date, net amount, and VAT rate.^[2]

Step 2: Reconcile Your Records

Before filing, reconcile your records against your bank statements to ensure all transactions are captured. Check for:

Missing sales invoices or purchase receipts
Incorrect VAT rates applied to transactions
Duplicate entries
Any adjustments needed (bad debt relief, fuel scale charges, etc.)

Step 3: Review the Nine-Box Summary

Your software generates the nine-box summary from your records. Review each box carefully:

Does Box 1 (output VAT) look reasonable given your sales?
Does Box 4 (input VAT) match your purchase invoices?
Is Box 5 (net VAT) the amount you expect to pay or reclaim?
Do Boxes 6 and 7 (net sales and purchases) align with your business activity?

Step 4: Submit to HMRC

Once you are satisfied with the figures, submit the return through your software. The software connects to HMRC’s MTD APIs and transmits the data securely. You will receive a confirmation with a unique receipt reference.

Step 5: Pay (or Receive) the VAT

If you owe VAT (Box 5 is positive), pay HMRC by the deadline — typically one calendar month and seven days after the end of the VAT period. If you are due a refund, HMRC will process it after reviewing the return.

Tip: Set up a Direct Debit with HMRC for VAT payments. This ensures you never miss a payment deadline and gives you an extra three working days to pay.

File Your VAT Return in Under 30 Seconds

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Authorising Your Software

Before filing your first MTD VAT return, you need to authorise your software to interact with HMRC:^[1]

Sign up for MTD — if you have not already, sign up for Making Tax Digital for VAT through your HMRC account
Link your software — in your MTD software, follow the prompts to connect to HMRC. You will be redirected to the Government Gateway to sign in and grant access
Authorise — confirm that the software can view and submit your VAT information

This authorisation only needs to be done once. After that, your software can file returns and retrieve obligations without you signing in to HMRC each time.

VAT Return Deadlines

MTD does not change your VAT return deadlines. The standard filing and payment deadline is one calendar month and seven days after the end of your VAT period:^[3]

VAT Period Ends	Filing & Payment Deadline
31 March	7 May
30 June	7 August
30 September	7 November
31 December	7 February

Your specific periods may differ if you use non-standard stagger groups. Check your HMRC account or software for your exact deadlines.

Correcting Errors

If you discover an error after filing your MTD VAT return:^[2]

Errors up to £10,000 (or 1% of Box 6 turnover, up to a maximum of £50,000) — adjust on your next VAT return
Errors above the limit — notify HMRC separately using form VAT652
Deliberate errors — must always be disclosed to HMRC regardless of size

How GoFile Files Your MTD VAT Return

GoFile is bridging software — it connects your existing records to HMRC without replacing your accounting system. Here’s the entire process:

Import Enter your nine-box figures or import from a spreadsheet

Review Check your totals — GoFile validates before submission

Submit One click — filed via HMRC’s official MTD API

Total time: under 30 seconds.

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Frequently Asked Questions

Has the VAT return changed under MTD?

No. The VAT return still contains the same nine boxes. What has changed is the method of submission: you must file through MTD-compatible software rather than the HMRC online portal. The figures, deadlines, and payment process remain the same.

How do I authorise my software to file to HMRC?

When you first set up your MTD software, you will be asked to grant it access to your HMRC account. This involves signing in to your HMRC Government Gateway account and authorising the software to act on your behalf. This only needs to be done once.

What if I make a mistake on my MTD VAT return?

If you discover an error after submission, you can usually correct it on your next VAT return (for errors up to £10,000 or 1% of turnover, whichever is greater). For larger errors, you must notify HMRC separately using form VAT652.

Can my accountant file my MTD VAT return for me?

Yes. Your accountant can use their own MTD-compatible software to file on your behalf, provided they are authorised as your agent with HMRC. Many accountants use agent services to manage MTD submissions for their clients.

Sources

Making Tax Digital for VAT — GOV.UK
VAT Notice 700/22: Making Tax Digital for VAT — HMRC
Submit a VAT return — GOV.UK
Find software compatible with Making Tax Digital for VAT — GOV.UK