Year-end guide for QuickBooks Online Payroll

If you pay employees weekly, fortnightly, or every four weeks and your last payday falls on 5 April, you’ll have an extra “Week 53” payroll.

• What it means: An extra payday within the tax year.
• How it affects taxes: Week 53 tax is calculated separately from total annual earnings.
• If you pay monthly: Week 53 does not apply.

For company directors using the alternative NIC method, QuickBooks will automatically adjust for Week 53.

QuickBooks will prompt you when it’s time. Before you run it, confirm employee details, tax codes, pay items and pension settings are correct.

If you need to edit or delete a pay run:

1. Click the ⚙️gear icon and go to Account and Settings.
2. Select Payroll Settings, then UK Tax.
3. Adjust your Employment Allowance if needed.

Your Full Payment Summary (FPS) tells HMRC how much tax and National Insurance has been paid. After submitting, wait for confirmation from HMRC.

Check your submission in QuickBooks:

• Follow this link to complete the steps in product
• Find your FPS submission and select Review.

Learn more about how to submit an FPS to HMRC in Payroll.

Employers must give employees payslips on or before their pay date. Payslips show earnings, tax deductions, and other contributions.

Make sure you're on top of your Employer Payment Record (P32) report. This report is a summary of the payments made HMRC each tax month, helping you assess whether you need to submit an EPS. It also includes details of PAYE, NI contributions and student loans deductions.

1. Follow this link to complete the steps in product
2. Search for P32 report.

When you’re ready to move into the new tax year:

1. Follow this link to complete the steps in product
2. Select Payroll Settings from your To Do List or Settings.
3. Choose Active Tax Year and select the new year (for example, 2025/26).
4. Select Save.

Changes that can only be made at the start of a new tax year:

1. Change how company directors’ National Insurance (NI) is calculated.
2. Update an employee’s pay schedule.
3. Change an enrolled employee’s pension scheme.

Once updated:

• P60 forms can be generated.
• Employment Allowance is reset.
• Make sure all employee details are correct before running payroll.

P60 forms summarise each employee’s total pay and deductions for the tax year.
You must issue P60s to all employees by 31 May following the end of the tax year.

And that's it! You've successfully completed your final payroll for this tax year.

If you need to move back to the prior tax year:

Follow this link to complete the steps in product

1. Check for payments made in the new tax year and delete any dated after 6 April.
2. Revert pay schedules and pension schemes to the previous year’s settings.
3. Reactivate and adjust any terminated employees before deleting payslips.
4. Review pension enrolments — Payroll removes pending enrolments when you advance to a new year.

1) “I can’t run payroll.”

Make sure you’re in the correct Active tax year in QuickBooks (⚙️ Settings → Payroll Settings → Active Tax Year). If you recently moved back a year, also re-check employee tax codes/NI letters are valid for that year.

2) “I’m getting a date error on the first pay period.”

This usually means your pay date or pay schedule doesn’t align with the selected tax year. Set the correct Active tax year, then confirm the first pay date. HMRC requires the FPS to show the actual payment date (not the date you ran payroll), and RTI filings must align to tax periods.

3) “Week 53/54/56 has confused the tax.”

If your final payday of the tax year falls on 5 April for weekly/fortnightly/four-weekly schedules, you may have an extra run (“Week 53”, etc.). Tax for that run is calculated on a non-cumulative (week 1) basis. That is expected behaviour under PAYE.

4) “Payslips weren’t issued on time.”

You must give payslips on or before payday (paper or electronic). Build this into your run workflow (approve → publish).

5) “P60s are late / employees are asking for them.”

P60s must be provided to all employees who were on your payroll on 5 April by 31 May. In QuickBooks, generate P60s after you’ve moved into the new tax year and finalised year-end.

6) “Tax code or NI details look wrong / are being rejected.”

• For new starters without a P45, use HMRC’s Starter Checklist to set the initial tax code; update the code when HMRC later issues a coding notice.
• If a P45 arrives after your first FPS for that employee, keep using the tax code you already reported until HMRC sends a new one.
• Rejections often come from mixing years (using a code or NI category letter not valid for that tax year) — confirm the Active tax year first.

7) “I need to fix something after submitting payroll (wrong pay/tax/NI).”

You can correct mistakes by sending a corrected FPS (and EPS where relevant), and adjusting in the next run if needed. HMRC has specific guidance on correcting submissions and payments; follow that flow, then re-issue payslips to affected employees.

8) “P45 details aren’t appearing on HMRC submissions.”

Check the employee’s hire date is in the correct tax year; then remove and re-enter the P45 details and save again. If the first FPS has already gone, keep the existing code until HMRC issues a new one.

9) “I can’t change a director’s NI method / an employee’s pay schedule or pension scheme.”

Those changes are typically restricted to the start of a new tax year in Payroll. Switch to the new year first, then update the settings before the director/employee is paid in that year.

10) “My PAYE bill looks off after realigning dates or making corrections.”

Mismatched FPS dates or period alignment can skew the PAYE/NIC position. Realign the FPS to the actual pay date and, if necessary, use EPS to correct period-level figures per HMRC guidance.