Processing VAT returns

VAT (Value Added Tax) is added to almost all goods and services in the UK. Some items and services are exempt or zero rated for VAT but the majority attract VAT at the standard or lower rate.

If your company is VAT registered then you need to submit a VAT return to HMRC every quarter. Our online application makes this easy for you – all you need to take care of is ensuring your records are up to date then you can approve your VAT return for submission.


We’d be delighted to check your books before you complete your first VAT return, this way you can be sure that you’re doing things right. All you need to do is send a copy of your bank statements covering the VAT return period to your account manager. They’ll check your transactions in inniAccounts before filing your return.

Step 1 – Update your books

Once your VAT period has ended your account manager will send you an email to let you know and you’ll see a message on your dashboard.

So we can file your VAT return, you’ll need to update your bookkeeping to the end of the VAT period so your bank balances in inniAccounts match exactly the balances on your bank statements. You’ll need to do this for each business account that you have – current, savings account and company credit cards. For further information on bookkeeping please see the following guides:

You need to complete your bookkeeping by the 15th of the month following the end of your VAT return period. For example, if your VAT return is for October to December you’ll need to complete your bookkeeping by 15th Jan.

Step 2 – Confirm books ready

When you’ve completed bookkeeping and the balances in inniAccounts matches your bank statements you can confirm to us your bookkeeping is up to date. Simply click on the “bookkeeping done” link on your company’ homepage:

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It’s really important that your bookkeeping in inniAccounts matches your bank statements exactly. If not your VAT return will be incorrect, which could lead to a fine or an investigation from HMRC.

If you overrun the VAT return deadline the reminder will turn red. You must complete your bookkeeping as a matter of urgency otherwise your return may be filed late. We cannot submit your VAT return until your bookkeeping is complete. If you’re having difficulties please contact your account manager for assistance.

Step 3 – Review & accept VAT return

When you click your ‘bookkeeping done’ button you’ll be shown your VAT return to review. Carefully check the return and its calculations (by scrolling down) then when you are happy click the button to approve the return.


It is important that you check the transactions at the bottom of your return to make sure everything you expect is listed for the VAT period. If you have applied the correct VAT percentages on your invoices, expenses etc you shouldn’t find any problems.

If you spot a problem simply press the ‘Redo bookkeeping’ button to cancel the VAT return then you can amend your transactions. If you need help, advice or are just not sure, before you approve your return contact your account manager who will be glad to help.

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Step 4 – Return ready for filing

Once you have clicked the button to approve your return you will see a confirmation message and your account manager will be notified. They will then complete some checks and submit your approved return to HMRC for you.

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Step 5 – Filing and payment

Once your account manager has filed your VAT return you will receive an email confirmation detailing what payment is due. You’ll also find a VAT payment reminder on your dashboard along with a new pending payment in your bookkeeping screen.

If you pay VAT via Direct Debit then the payment will be collected on or around the 10th of the second month following the end of your VAT period. For example, for a VAT return covering the period October to December the payment will be taken around 10th February.

Payments of VAT by methods other than Direct Debit should be paid to HMRC before 7th of the month using these account and payment details.


If a Direct Debit has been setup, please do not pay your VAT by any other method. If a payment hasn’t been taken by the 14th please get in contact with your account manager and they will investigate for you.