If payroll has been processed and FPS(s) have been submitted to HMRC using an incorrect NINO, you will need to correct the records with HMRC by zeroing out all submissions under the wrong NINO and resubmitting them under the correct one. Before making any changes, take a record of all payroll processed under the incorrect NINO — this could be copies of the employee's payslips or a payroll summary report from the Analysis section.

Step 1 — Zero out submissions under the incorrect NINO

Starting with the oldest pay period in the tax year, reopen the payslip and zeroise all pay elements. Finalise the payslip, then submit an Additional FPS for that employee only:

• Go to RTI > New > Additional FPS
• Click Select None at the top of the screen, then tick only the affected employee
• On the right-hand side, ensure the Late Reporting Reason is set to Correction to Earlier Submission
• Click to create and submit to HMRC

Return to the Payroll tab, select the next period, zeroise all pay elements, finalise, and submit another Additional FPS correction for that employee for this period. Repeat this process for every pay period, working from oldest to newest. This ensures the year-to-date figures are updated progressively, effectively removing all incorrect earnings from that NINO in the PAYE scheme.

Step 2 — Resubmit under the correct NINO

Once all periods have been zeroed out under the incorrect NINO, reopen the oldest pay period again and re-enter the pay details using the records you took at the start. Now go to the employee's record and update the NINO to the correct one. Return to Payroll, finalise the first period, and submit an Additional FPS > correction to earlier submission for that employee only. Continue period by period — entering the correct pay details, finalising, and submitting an Additional FPS correction for each period before moving on to the next pay schedule — until all periods are up to date under the correct NINO.

From this point forward, payroll can be processed as normal using the correct NINO.