When You Realise an Employee’s Payroll Was Wrong — After You’ve Already Submitted PAYE

You’ve clicked “Submit,” sent your PAYE to HMRC, and finally taken a breath. Then you realised: “Oh, one of the employees already left last month. I made a mistake. How to correct it? Should I re-submit the corrected version now? What I should do?” OR “the payroll amount for employee A is entered wrongly; it is £2xxx instead of £1xxx. How can I correct it? Deadline is tomorrow, I shall create a new submission before the deadline? Shouldn’t I?)

PAYE Mistake, Sound familiar?

Now you’re thinking — can I just delete it? Submit again? Re-upload the corrected version? Let me explain to you step by step in depth.

Once You’ve Submitted PAYE, Can You Change It?

When your PAYE (through your Full Payment Submission, FPS) has already been sent to HMRC, that data becomes part of their live record. You can’t just overwrite it, delete it, or “resend” the same month again with different figures.

If you try, HMRC’s system may interpret it as a duplicate submission — sometimes creating two versions of the same record. That can cause endless confusion in PAYE calculations, employee tax codes, and even your PAYE bill itself. Even HMRC’s own Basic PAYE Tools doesn’t allow you to simply “delete” or “replace” a previous submission once it’s gone through. The only reliable and compliant way is to adjust the information in the next submission.

How to Correct Wrong PAYE Submitted?

So people wonder how to correct wrong submission of PAYE. It is not re-submission of zero against the wrong one already submitted. Doing so will create duplication of the PAYE submission, and without your knowledge, your tax and NIC liability will double somehow. It is not the right way for correction. So how to correct wrong PAYE submission. HMRC guideline is clear and simple, yet powerful, “To correct a mistake made in the current tax year, update the year-to-date figures in your next regular FPS.” That’s it. You don’t resend, you don’t delete, and you don’t start a new PAYE file. You just carry forward the corrected year-to-date numbers.

Okay, it sounds easy. That’s right. It is easy. What’s about if this is the last month of the tax year. The handling may be different. What about the mistake is EPS for employer? Handling and correction may be a bit different from description above. It depends on systems you are using. Most of the commercial solution allows this option.

But What If It’s the Final Month of the PAYE Year?

If you discover the issue before the final submission (say, in March), just make the correction in that month’s FPS — HMRC will read the updated year-to-date figures automatically.

If, however, you’ve already submitted your final FPS for the tax year (for example, the employee error is discovered in May, long after April’s final payroll), then you’ll need to file a Year-End Amendment FPS — an additional correction submission specifically designed to update the previous year’s data.

It’s not difficult, but it does have to be done carefully to avoid creating duplicates.

PAYE Mistake, Then What About Tax and NIC Calculation ?

Once you realise a mistake. And correct it according to above method. Tax for employee and NIC will be re-calculated to reflect correct amount. So you do not need to worry. Then what about employer portion of national insurance. For many small to medium sized employer they may have applied employment allowance and get it reduced, it may make the picture a bit more complicated than it should. And you may not know, the calculated and paid employer portion of national insurance contribution, it may not be recovered after the correction. And the exemption reduced by employer allowance may not be recovered as a result. But luckily, if you are lucky, there is no actual damage as the employer portion may well be covered by the allowance. But the allowance limit is thus reduced by the wrongly calculated portion. So there is good news and bad news.

What If PAYE Mistake is in an Older Year?

Mistakes from older tax years — say 2019–2020 — can still be fixed. HMRC allows you to correct even historical submissions by sending an additional FPS for that tax year, or in some older cases, by submitting an Earlier Year Update (EYU).

So even if you uncover something months (or years) later, there’s usually a route to correct it properly. It’s all about matching the correction method to the relevant tax year.

Still Confused How to Handle PAYE Mistake ? You’re Not Alone

Payroll is one of those areas where a small oversight — a wrong date, an employee marked active instead of a leaver, or a mis-keyed amount — can spiral into a tangle of confusion.

But don’t worry — when there’s a question, there’s always an answer.

That’s what our blog is here for: to help business owners, bookkeepers, and fellow accountants navigate the practical realities of UK payroll and tax. We regularly share step-by-step guidance, tips, and explanations on how to handle both the straightforward and not-so-straightforward cases.

Seek Professional Help

If you’re unsure how to handle a payroll correction or PAYE adjustment, speak to your accountant before resubmitting anything. At Elaga Accountancy, our experienced UK tax advisers deal with all types of payroll corrections — from simple pay adjustments to complex multi-year reconciliations. Let us handle your tax matters so you can focus on what you do best — running your business and making money.

Get in touch today and let’s make your payroll smooth, compliant, and stress-free.

***Contact us to learn more.

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