How Do I Pay My Tax Bill Once I Have Submitted My Return

At Towerstone Accountants we provide specialist personal tax services, for self employed, and individuals across the UK. This article has been written to explain How do I pay my tax bill once I have submitted my return, in clear practical terms, so you understand how personal tax and Self Assessment rules apply in real situations. Our aim is to help you stay compliant, avoid costly mistakes, and make confident tax decisions.

This is one of those questions that usually comes right after a moment of relief. You submit your Self Assessment return you finally see the figures clearly and then the next thought is what now and how do I actually pay this.

From my experience as a chartered accountant specialising in Self Assessment this is the point where people either feel back in control or suddenly overwhelmed again. The good news is that paying your tax bill is usually far more straightforward than people expect once you understand the options and the deadlines.

In this article I want to walk through exactly what happens after you submit your return how HMRC tells you what you owe the different ways you can pay and what to do if you cannot pay it all at once. This is based on real UK processes and the situations I deal with every year with clients.

What happens immediately after you submit your tax return

Once your Self Assessment return is submitted HMRC calculates your tax bill automatically. If you file online this calculation appears almost instantly.

You will see a breakdown showing income tax National Insurance and any student loan repayments if applicable. You will also see the total amount due and the payment deadlines.

In most cases the key date is 31 January following the end of the tax year. This is when any balancing payment is due. Depending on your circumstances you may also see a payment on account due at the same time and possibly another one due on 31 July.

From experience this is where confusion often starts. People focus on the total figure without understanding what it represents. That is why I always recommend reviewing the calculation carefully rather than jumping straight to payment.

Understanding what you are actually paying

Your tax bill may include more than just tax for the year you have just reported.

It can include the balancing payment which settles any remaining tax for the year just ended. It may also include payments on account which are advance payments towards the following tax year.

Payments on account catch many people out especially in their first or second year of self employment. They are not penalties or extra tax. They are simply advance payments based on the assumption that your income will be similar next year.

If your income is falling these can often be reduced but that should be done carefully.

How HMRC expects you to pay

HMRC does not automatically take payment when you submit your return. You must actively make the payment.

In my experience most people pay online and HMRC offers several methods. The most common is online banking. You log into your bank set HMRC up as a payee and make a transfer using your unique reference number.

That reference number is crucial. It ensures the payment is allocated to your account correctly. Paying without it can cause delays and unnecessary stress.

You can also pay by debit card through your HMRC online account. This is instant but some people prefer bank transfer for larger amounts.

Other options exist such as direct debit or paying in instalments but these are less commonly used for one off payments.

Paying by bank transfer in practice

This is the method I see used most often.

You make a payment to HMRC using their bank details which are published on GOV.UK. You include your Self Assessment reference as the payment reference. This usually starts with UTR followed by K.

Payments made this way typically reach HMRC the same day or next working day depending on your bank.

From experience I always advise clients not to leave this until the last minute particularly in January when banking systems and HMRC processing can be under pressure.

Paying through your HMRC online account

If you are logged into your HMRC account you can see your balance and make a payment directly.

This can be reassuring because you can see the payment reflected against your account. It also reduces the risk of using the wrong reference.

This method works well for people who like visibility and confirmation.

What if you cannot pay the full amount straight away?

This is one of the most important points to understand.

HMRC would rather you engage than ignore the bill. If you cannot pay in full you should not panic but you also should not do nothing.

In many cases you can set up a Time to Pay arrangement online if your debt is under a certain threshold and you are within a short period after the deadline. This allows you to spread the cost over monthly instalments.

For larger debts or more complex situations HMRC will usually require a conversation. This is where having an accountant helps because the proposal needs to be realistic and supported by figures.

From experience HMRC is far more receptive when approached early and honestly.

Interest and penalties to be aware of

If you pay after the deadline interest will be charged from the due date until payment is made. Interest rates change so it is important to check the current rate.

Late payment penalties can also apply if the tax remains unpaid for a period of time. These are usually a percentage of the outstanding balance and increase the longer the debt remains.

This is why even partial payment can help. Paying what you can reduces interest and penalties while you arrange the rest.

Common mistakes I see people make

One common mistake is assuming HMRC will automatically take payment. They will not unless you have set up a direct debit in advance.

Another is misunderstanding payments on account and thinking they are errors. This often leads to delayed payment while people query something that is actually correct.

I also see people pay the wrong amount or use the wrong reference which creates unnecessary confusion later.

All of these issues are avoidable with a bit of guidance.

How an accountant helps at this stage

This is where the value of an accountant really shows.

An accountant will explain exactly what the bill consists of confirm deadlines and advise on the best payment method. If cash flow is tight they can help decide whether a Time to Pay arrangement is appropriate and deal with HMRC on your behalf.

In my experience this turns a stressful moment into a manageable process.

Key points to takeaway

Paying your tax bill after submitting your return is usually straightforward once you understand what you are paying and when it is due. The key is not to rush blindly or ignore the figures.

Review the calculation understand whether payments on account apply and choose a payment method that works for you. If you cannot pay in full engage with HMRC early rather than hoping the problem will disappear.

From experience the people who stay calm and proactive almost always find the situation far easier to deal with than they expected.

You may also find our guidance on How can I set aside money for my tax bill each month, and Can HMRC take money directly from my account, helpful when reviewing related personal tax questions. For a broader overview of Self Assessment deadlines, reporting, and obligations, you can visit our self assessment guidance hub.