Navigating the world of VAT payments can feel like traversing a complex maze. But with the right tools and guidance, you can find the most efficient path through the labyrinth. In this comprehensive guide, we’ll provide you with the key information needed to confidently make your VAT payments online and keep your business running smoothly.

When do you need to pay your VAT bill?

Most businesses need to complete a Return every quarter, this includes the more lucrative small business. The deadline for submission and payment is typically one month and seven days after the end of the specified period. For example, if the three-month period ran from January 1st to March 31st, your Return and payment would be due by May 7th. Your quarterly dates will operate on a rolling cycle and do not necessarily have to be tied to a calendar year. It is usually helpful to choose quarters that are co-terminus with your year end.

VAT Registration

To register, businesses need to apply through the UK Government Gateway. Registration can be quite complex and so we would recommend appointing an accountant to complete the registration process on your behalf to ensure that it is completed accurately. Common examples we see where clients have attempted to do the registration themselves include registering earlier than necessary (and therefore having to pay more Value Added Tax and sooner) or registering for a scheme that isn’t cost effective for them.

VAT Payment Methods

HMRC offers several payment methods to settle your bill:

  1. Online or telephone banking (using the Faster Payments service)
  2. CHAPS (Clearing House Automated Payment System)
  3. Direct debit
  4. BACS (Bankers’ Automated Clearing Services)
  5. Debit or corporate credit card using BillPay
  6. Standing order (only for businesses using the Annual Accounting Scheme)

We would recommend that all businesses pay by direct debit. This is because it then takes away the headache of having to remember to pay the VAT, but it also means that the business receives an additional 3 working days before the VAT is paid.

How to Pay Your VAT Online

  1. File your Return through your online account or use Making Tax Digital (MTD)-compliant software.
  2. Pay using your preferred payment method.
  3. Check your online account to see if your payment was received within 48 hours.

Record Keeping for VAT Filing (Using Xero)

Xero is a popular cloud-based accounting software that can help streamline record keeping for VAT filing. It’s the software we’d recommend all e-commerce businesses use to maintain their bookkeeping records. With Xero, businesses can efficiently manage their finances, monitor transactions, and file returns directly to HMRC. Here’s how Xero can help your business with compliance:

1. Automatic VAT Tracking

Xero automatically tracks and calculates VAT on sales, purchases, and expenses, making it easier to keep accurate records. By connecting your bank account to Xero, you can quickly reconcile transactions and monitor transactions in real-time.

2. VAT Reporting

Xero offers comprehensive VAT reporting features, allowing you to generate summaries, detailed reports, and audit reports. These reports can help you analyze your transactions and prepare your VAT Return.

3. Making Tax Digital (MTD) Compliance

Xero is fully MTD-compliant, which means you can easily file your VAT Returns directly to HMRC through the platform. This seamless integration with HMRC’s systems helps reduce the risk of errors and ensures that your business is compliant with UK tax regulations.

4. Cash Flow Management

Xero’s cash flow management tools enable you to monitor your business’s financial health and ensure that you have enough funds to pay your VAT bill on time. You can create budgets, forecast cash flow, and set up alerts for upcoming VAT deadlines.

5. Integrations and Add-Ons

Xero offers numerous integrations and add-ons designed to streamline your business’s financial management. You can connect Xero with e-commerce platforms (we’d recommend doing this via A2X), inventory management systems, and other productivity tools to further enhance your record keeping for VAT filing.

6. Access Anywhere, Anytime

As a cloud-based software, Xero can be accessed from any device with an internet connection, making it easy to manage your finances and VAT compliance on the go. This flexibility allows you to stay on top of your business’s financial health and obligations, even when you’re away from the office.


1. What happens if your payment is late?

You may face penalties or surcharges, which are calculated based on a penalty points system (a bit like driving licence points)

2. Is VAT compulsory to pay?

VAT is compulsory for businesses with a taxable turnover above the VAT registration threshold (£85,000 as of 2023).

3. How long do you have to pay VAT?

Payment is typically due one month and seven days after the end of the specified period.

4. Can I defer my payments?

If you cannot pay on time, contact HMRC’s business payment support service to arrange a payment schedule and minimise penalties.

5. Does VAT get refunded?

If you’re owed a VAT repayment from HMRC, you’ll usually be paid within 30 days by direct deposit (if HMRC have your bank details) or cheque.

Final Thoughts on Paying VAT

Paying VAT is an essential part of running a successful e-commerce business in the UK. By understanding when and how to pay VAT online, registering on time, choosing the right payment method, and keeping accurate records, you can avoid penalties and ensure smooth financial operations.


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