Last updated: 16 October 2026
What is payroll hygiene?
Payroll hygiene means keeping the data you send to HMRC through Real Time Information (RTI) accurate and consistent. HMRC matches every Full Payment Submission (FPS) to an employee record using their name, date of birth, National Insurance number and payroll ID. If any of these change unexpectedly, HMRC’s system can open a second employment for the same person. The result is wrong tax codes for the employee and an inflated PAYE bill for you.
How duplicate employments happen
Say William earns £2,000 a month. His payroll ID is 001. After a software change his ID becomes W001, but no leaving date is sent for 001. HMRC now thinks William has two jobs. It expects PAYE on both, issues a BR or 0T code for the “second” job, and your HMRC account shows a debt that you do not owe.
Common causes
- Changing payroll software and not carrying over payroll IDs
- Re-using a payroll ID for a different employee
- Re-employing a leaver under a new ID without marking the old record as ceased
- Missing or wrong National Insurance numbers
- Sending a leaving date in the wrong pay period, or not at all
- Mixing up the “payroll ID changed” indicator
How to fix a duplicate
- Compare your FPS figures with the liabilities in your HMRC business tax account.
2. If an employee appears twice, send an FPS for the old record with a leaving date and year-to-date figures of zero, or use the “payroll ID changed” indicator with the old ID on the next FPS.
3. Check the employee’s tax code notices and ask HMRC to correct them if needed.
4. If the debt remains, contact the HMRC Employer Helpline with the details.
Good payroll habits
| Habit | Why it helps |
| Keep one payroll ID per employment | Stops duplicate records |
| Send leaving dates on time | Ends the employment on HMRC’s records |
| Check NI numbers at onboarding | Avoids mismatches with DWP records |
| Send an EPS for months with no pay | Stops HMRC estimating a charge |
| Reconcile your HMRC account monthly | Spots errors before penalties or interest |
Why it matters in 2026/27
Employer National Insurance is 15% above the £5,000 secondary threshold, so a duplicate record can create a large phantom bill. HMRC charges late payment interest at 7.75% a year (Bank of England base rate plus 4%) on genuine underpayments, and penalties apply for late filing and late payment. Also, from April 2027 most benefits in kind must be reported through payroll, which will make accurate RTI data even more important.
Frequently asked questions
Can a duplicate employment affect the employee?
Yes. They may get an emergency or BR code and pay too much tax until HMRC corrects it.
Should I pay the extra PAYE HMRC shows?
No. Pay what your FPS shows is due and get the duplicate corrected, keeping a record of your calls.
How long does HMRC take to fix it?
Corrections sent by FPS are usually picked up within a few weeks.
Will changing payroll software cause this?
It can, unless the new software carries over the old payroll IDs or you use the ID-change indicator.
Related: what RTI is, missed PAYE payment deadlines and new employees with no P45.
Talk to Accotax
Want this handled for you? Our team at Accotax can help with payroll and RTI reporting. See our payroll services service, or contact us for a free, no-obligation quote.
This page is general guidance based on HMRC rules for the 2026/27 tax year, checked against gov.uk on 16 October 2026. It is not personal advice, so speak to an accountant about your own situation.
