Think you’ve paid too much tax? A guide for the Self-Employed

12th March 2026
Written by Qdos

Think you’ve paid too much tax?

Tax is rarely simple, and if you’re self-employed, it can be easy to overpay without realising. Whether your income dipped, your expenses weren’t fully claimed, or you made an honest mistake on your return, here’s what to do if you think you’ve paid too much and how to claim it back.

 

 

Why might I have overpaid tax?

There are a few common reasons why self-employed people might end up overpaying tax. One of the most frequent is when your income ends up being lower than expected, but your payments on account (the advance payments HMRC asks for based on last year’s tax bill) were based on a higher figure. If your earnings drop significantly, this can lead to you paying more than you owe.

You might also overpay if you’ve made a mistake on your tax return. For example, by overstating your income or forgetting to claim allowable expenses. This is just one of the reasons good record-keeping is so important!



Does HMRC refund overpaid tax if you pay through Self Assessment?

Yes, HMRC does refund overpaid tax. If you overpay through the Self Assessment system, HMRC will usually issue a refund automatically once your tax return is processed. You’re able to state in your tax return how you’d prefer to have any money you’re owed paid to you; either directly into your bank account, or by cheque. 

If you have upcoming payments on account in the next 45 days (e.g., for the next tax year), HMRC may apply your overpayment to those instead of refunding it. 

In some circumstances, you may need to prompt HMRC to issue a refund. For example, if the amount is small, or if you haven’t stated how you’d like to receive payment on your tax return. If you file your tax return online, you can prompt a repayment by logging into your HMRC digital services account and clicking ‘Request a repayment’.  

Read more: Six Tips to Complete Your Self Assessment on Time, Every Time!



What to do if you’ve made a mistake on your Self Assessment tax return

If you realise you’ve made a mistake on your tax return, you can usually correct it by submitting an amended tax return to HMRC. This can be done online if you filed your original return digitally (using the portal where you originally submitted your Self Assessment), or by paper if you submitted it that way. Remember, though, if you want to amend a tax return, you’ll have to provide supporting evidence as to why you’re making the change.

 

 

Time limit for tax return corrections

Generally speaking, tax returns can only be corrected up to 12 months after the Self Assessment deadline for the relevant tax year. However, if you believe you have overpaid tax, you may be able to claim overpayment relief beyond this 12-month window. 

Overpayment relief allows you to request a refund for tax paid in error or over and above what you owe, even if the usual deadline for amendments has passed. To qualify, you’ll need to provide evidence, and you should make your claim as soon as possible. Keep in mind that HMRC may take longer to process these claims, and the rules can be more complex, so it can be a good idea to get professional advice if you think you’re eligible. 



What happens after I’ve requested a refund from HMRC?

Once you’ve submitted your return or amended it and requested a repayment, HMRC will usually take a few days to a few weeks to process it. If you’re due a repayment and haven’t received anything after a few weeks, it’s worth logging into your HMRC account to check the status, or giving them a call.

If HMRC is applying your overpayment to future tax liabilities instead, this should be clearly shown in your account as a credit.



What if HMRC wants more than you think you’ll owe?

HMRC bases your Payments on Account on your previous year’s tax bill, essentially assuming your income and circumstances will stay the same. But if your situation changes, that estimated amount might be too high.

For example, you may end up owing less tax if:

 

  • Your business profits fall
  • You become eligible for more tax relief
  • More tax is deducted at source than in the previous year

If you think your upcoming tax bill will be lower, you can ask HMRC to reduce your Payments on Account. You can do this through your online Self Assessment account or by submitting form SA303.

Just be careful - if you reduce your payments too much and end up owing more, you may be charged interest on the difference. It’s always worth speaking to an accountant or tax advisor if you’re unsure.

The best way to avoid overpaying is to keep your bookkeeping up to date and review your income regularly, especially before submitting your tax return or agreeing to HMRC’s suggested Payments on Account. If your income is fluctuating a lot, consider working with a tax advisor or accountant who can help you stay on top of your obligations (and opportunities to save!)
Qdos Contractor
Written by
Qdos
Qdos is an award-winning provider of insurance for the self-employed and a leading authority on IR35. Our industry-leading employment status services help the flexible working sector thrive. Our accolades include Best Contractor Insurance Provider 2024, Best Legal, Compliance or Tax Adviser 2025, the Queen’s Award for Enterprise in Innovation in 2017 and 2022, and the Feefo Platinum Trusted Service Award 2026.

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