Incorrect Tax Codes in UK Payroll: Causes, Risks and How Employers Can Fix Them

Are you confident every employee on your payroll is using the correct tax code?

For many UK businesses, the honest answer is “probably, but we haven’t checked recently.” Unfortunately, incorrect tax codes are one of the most common causes of payroll errors, leading to employees paying too much or too little tax through PAYE.

The challenge is that tax code errors often go unnoticed. A wrong code can remain in your payroll system for months, producing incorrect deductions every pay period until an employee raises a concern or HMRC identifies the issue through Real Time Information (RTI) submissions.

Whether the problem stems from an outdated HMRC notice, an emergency tax code that was never updated, or incorrect employee information, the result is the same: payroll inaccuracies, additional administration, and potential compliance risks for your business.

Understanding how tax code errors occur and how to prevent them is essential for maintaining accurate UK payroll and avoiding costly corrections later.

Key Takeaways

• Incorrect tax codes in UK payroll can lead to employees overpaying or underpaying tax, creating compliance and administrative issues for employers.
• Common payroll tax code errors involve codes such as 1257L, BR, 0T, D0, W1/M1, and NT when they are applied incorrectly or not updated.
• Tax code mistakes often occur because of missed P6 or P9 notices, emergency tax codes, multiple employments, or unreported benefits in kind.
• Incorrect tax codes can result in payroll corrections, employee complaints, HMRC enquiries, and additional PAYE liabilities.
• HMRC identifies tax code discrepancies through PAYE records and Real Time Information (RTI) submissions.
• Employers should regularly review tax codes, process HMRC notices promptly, and check payroll records before the start of each tax year.
• A consistent payroll process helps reduce the risk of tax code errors and improves payroll accuracy across the business.

Understanding PAYE Tax Codes and Their Impact on Payroll

Every tax code you apply in payroll directly determines what HMRC receives and what your employee takes home. It is the instruction your payroll software follows to calculate deductions.

Get it wrong, and every subsequent pay run produces the wrong result.

According to GOV.UK’s rates and thresholds for employers 2026 to 2027, the standard tax code for 2026/27 remains 1257L, reflecting a personal allowance of £12,570.

As GOV.UK’s guide to understanding your employees’ tax codes explains, when an employee’s circumstances change, HMRC emails the employer and updates the code through PAYE Online via:

• A P6 notice for in-year updates
• A P9 notice for new tax year updates

When those notices are not actioned, the old code keeps running.

The table below shows the codes most likely to cause problems when misapplied, as set out in GOV.UK’s guidance on what tax code letters mean:

The Five Most Common Causes of Tax Code Errors in UK Payroll

Tax code errors are rarely the result of negligence. They happen because UK payroll has a lot of moving parts, and a small delay in the right place creates a problem that takes months to surface.

Here are the five causes that come up most often.

Failing to Action P6 and P9 Notices on Time

As GOV.UK’s guidance on tax code changes during the tax year confirms, HMRC emails employers when a tax code changes. The new code must then be updated in the payroll record before the next pay date.

When P6 notices go unread, or a P9 bulk update is not applied before April, the old code keeps running. Every payroll run after that point produces the wrong deduction.

Leaving New Starters on Emergency Tax Codes

As GOV.UK’s guidance on emergency tax codes makes clear, emergency codes such as 1257L W1, 1257L M1, or 0T are applied when a new employee starts without a P45. HMRC notes this process can take up to 35 days to resolve.

The problem is that “temporary” often becomes permanent by accident. If the correct code is not applied once the employee’s details are confirmed, they can overpay tax for months without either party realising it.

Not Reflecting Benefits in Kind Within the Tax Code

Taxable benefits need to be reflected in the employee’s tax code so the right amount of tax is collected through payroll each month. Common examples include:

• Company cars
• Private medical insurance
• Season ticket loans

When they are not coded in, HMRC adjusts at year-end. That adjustment can arrive as an unexpected demand for both the employer and the employee.

Incorrectly Managing Tax Codes for Employees with Multiple Jobs

As set out in GOV.UK’s guidance on tax code letters, the BR code is used for a second job or pension. All income from that employment is taxed at the basic rate with no personal allowance applied.

Without the right setup across both employments, two things can go wrong:

• The personal allowance gets applied twice, causing underpayment
• The personal allowance is not applied at all, causing overpayment

RTI reconciliation will surface the discrepancy either way.

Carrying Outdated Tax Codes into a New Tax Year

According to HMRC’s P9X guidance on tax codes to use from 6 April 2026, the personal allowance stays at £12,570 for 2026/27.

Employers should copy the authorised code from the previous year’s record but must not carry over any W1 or M1 markings.

As GOV.UK’s guidance on updating codes for the new tax year also confirms, HMRC contacts employers between January and March about any new codes to use from April.

Individual employee codes may still need updating based on changed circumstances. If that review does not happen before April’s payroll runs, errors are locked in from the very first pay date of the new year.

How Incorrect Tax Codes Affect Your Business?

A wrong tax code is not just a problem for the individual on the payslip. It creates a chain of consequences that land squarely on your business.

• HMRC Demands and Interest Underpaid PAYE triggers a formal demand with interest. Persistent errors increase the risk of a formal compliance review or a full PAYE audit.
• Payroll Reprocessing Correcting a mid-period error means rerunning payroll, issuing revised payslips, and communicating with affected employees. That creates unplanned administrative workload.
• Employee Complaints Staff who discover they have been overpaying tax or receiving the wrong net pay lose confidence in your payroll process quickly. Some will raise formal HR complaints.
• Unexpected Cash Demands An HMRC demand for underpaid PAYE does not arrive with much warning. For businesses with tight margins, an unplanned tax liability creates real short-term pressure.
• RTI Flags and Audit Risk As confirmed by GOV.UK’s PAYE Online guidance, HMRC monitors employer submissions and sends alerts when reports are late or incorrect. A pattern of mismatches increases the likelihood of a formal review.

How to Prevent Tax Code Errors: A Practical Step-by-Step Process

Most payroll tax code errors are preventable. They do not require expensive software or a dedicated compliance team. They require a consistent process that makes tax code management a routine part of how payroll runs.

1. Check PAYE Online Regularly

As GOV.UK’s PAYE Online guidance confirms, tax code notices including P6 and P9 are accessible directly through your business tax account. Build a weekly check into your routine so nothing sits unactioned.

2. Set Up New Starters from Day One

Always collect a P45 or complete the starter checklist before the employee’s first pay date. Their answers determine the correct code from the outset and reduce the risk of defaulting to an emergency code unnecessarily.

3. Review All Tax Codes Before April

Check all employee codes against HMRC’s P9 update before the first pay run of the new tax year. Do not leave this until after April’s payroll has already gone out.

4. Monitor High-Risk Employees More Frequently

Those with multiple jobs, taxable benefits, or recent changes to their circumstances need more careful monitoring. Review their codes at least once a quarter.

5. Train Your Team on P6 and P9 Notices

Knowing when to update a code and when to wait for a formal HMRC instruction prevents most of the delays that cause errors.

As GOV.UK’s guidance on correcting a wrong tax code confirms, once a correction is submitted, HMRC will update the code and notify both the employer and employee within 15 working days.

For businesses that do not want to manage this in-house, outsourcing to an HMRC-compliant provider means coding notices are actioned as standard.

Outbooks handles the full PAYE cycle, from new starter setup through to year-end submissions, so tax codes stay accurate without the burden falling on your internal team.

Conclusion

Wrong tax codes do not fix themselves. Each missed notice or unchecked code runs through every pay period until HMRC raises a query or an employee notices something is off. The fix is consistent process, not complexity. Action P6 and P9 notices as they arrive, set new starters up correctly from day one, and review all codes before April. Those three steps prevent the vast majority of errors before they reach RTI.

If your team does not have capacity to manage PAYE coding notices consistently, Outbooks handles the full cycle icluding new starter setup, in-year updates and year-end submissions, so errors don’t build up quietly in the background.

FAQs

What is a tax code and how does it affect payroll?

A tax code tells your payroll software how much of an employee’s income is tax-free. Apply the wrong one and every deduction is incorrect HMRC will identify the gap through RTI.

What are the most common tax code errors UK employers make?

Not actioning P6 and P9 notices, leaving new starters on emergency codes after their details are confirmed, and failing to reflect taxable benefits in employee codes are the three most frequent causes.

What is an emergency tax code and when is it used?

Emergency codes such as 1257L W1/M1 or 0T apply when a new employee joins without a P45. They should be replaced with the correct code once the employee’s details are confirmed with HMRC.

What is the BR tax code and why is it sometimes applied incorrectly?

BR taxes all income at 20% with no personal allowance and is designed for second jobs. Applied to a primary employment, the employee overpays tax from their very first payslip.

What happens if HMRC identifies a tax code error during a payroll audit?

HMRC raises a demand for underpaid PAYE plus interest. Where errors show a pattern or lack of reasonable care, penalties can follow and the scope of the review may widen.

Can an employee check or challenge their own tax code?

Yes, through their Personal Tax Account on GOV.UK. The employer must still apply whatever code HMRC formally issues and cannot override it at the employee’s request.

How do P6 and P9 notices from HMRC work?

A P6 updates an individual employee’s code during the tax year. A P9 is the bulk update issued before 6 April. Both must be applied via PAYE Online before the next pay run.

Should UK businesses consider outsourcing payroll to reduce tax code errors?

If your team lacks capacity to manage coding notices and new starter processes consistently, outsourcing makes sense. A provider like Outbooks handles notices, new starter setup, and RTI submissions as standard.