If there is a mistake in a previous pay-run for 1 or more employees and this affects the amount of taxes due to HMRC, you will need to undo all periods back to (and including) the incorrect period for these employees. 

You can then re-process each period with the correct figures and submit the FPS once the final period is re-processed.

If you import payroll into accounts you will need to adjust the HMRC bills and/or the employee wage bills and/or pension bills in the Accounts module.

This is only supported for the current tax year as HMRC will not accept FPS submissions beyond 19th April

Step 1.

Navigate to Payroll > Overview, click on the appropriate payroll frequency and select the most recent period that was processed.

In this case, the most recent period is January.

Step 2.

To undo payroll calculations tick the check-box beside each appropriate employee and hit the Undo selected button.

Step 3.

Use the filters at the top to go back to the previous period. Repeat step 2 to undo the payroll calculation. 

Repeat this process up to an including the incorrect period. This must be done backwards in chronological order.

Step 4. 

You can now re-process the wages in each period for the employee(s). This must be done in chronological order.

Once you have processed the wages up to the most recent period, you can re-submit the FPS. This will send HMRC the adjusted YTD figures.

Fix problems with running payroll - You made a mistake in your FPS or EPS

Payroll Imported into Accounts

If you import payroll into accounts, you will need to adjust the wage bills and/or the HMRC bills and/or pension bills if there are any changes caused by the corrections above.

If the bills are paid, you will need to de-allocate the payments. This will move the bill back to the unpaid tab where you can edit and make necessary changes.

Alternatively, if you have underpaid you could create a new bill for the difference.