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Payroll Year End 2019/2020 for QuickBooks Online Standard Payroll

2019/2020 is almost behind us, but we want to ensure that you have all of the tools needed to sail smoothly into 2020/2021!

Things to keep in mind

Before you're ready to run your final payroll of the tax year, you need to make sure that the pay run is ready to go.

Now is a great time to take a look at your employee detail list, and make sure you have the correct information for each employee profile in the software.

A few things to keep in mind:

  • Have any employees left, or joined your business in this pay period? If there are, make sure you've processed the leaver or add new employees to your payroll (add employee)
  • Are there any absences, such as sick pay or any statutory payments, that are not yet entered? Make sure you've processed them if so
  • Do your employees want to receive their payslips and reports by email? If so, update your employee details

Quick Tip:

To verify your employee details, select Reports in the left menu in QuickBooks, and select the Employee Details Report. You can include the information most important to you by clicking on Display columns, and selecting the desired fields. You can even export it to Excel, CSV, PDF, or just view it in your browser.

If you process weekly, bi-weekly or four weekly payrolls, you may have to process week 53 as your final pay run. If your pay date falls on the 4th or 5th of April you might find your tax period is Week 53. This isn’t anything unusual, it’s just a method of ensuring that any deductions are in line with the 2019/2020 tax year.

Learn more about week 53.

In the event that you have multiple pay schedules, each schedule is handled independently of the other schedules, so remember to complete your final pay run for each of them.

Quick Tip: Not certain what tax period you’re in? Go to Employees or Payroll menu in QuickBooks, select Pay Runs tab and check the Tax Period column.

Process your final payrun

Now that you’ve check everything you need to, here is how to run your final pay run.

This article provides step by step instructions on how to process your final payrun. If you have multiple pay schedules, select whichever pay schedule you want to run first, and make sure that you're happy with the values before finalising the pay run.

Quick tip: When finalising your pay run, you can save time by submitting your Full Payment Submission (FPS) to HMRC, and even publish your payslips. Simply select the desired options before hitting “Finalise”.

P60s and year end reporting will be generated once all payruns have been finalised for the tax year.


You now need to submit your Employer Payment Summary (EPS) to HMRC for the year. Go to Taxes on the left menu in QuickBooks, and then Payroll Tax. If you need to submit an EPS, you will see it in the Due Now section.

Quick tip: Save time by saving your Government Gateway credentials in Company Settings.


Your employees need to be given a P60 before May 31st. You can download the P60 reports once you have ran your final payroll, or you can retrieve them individually from the Documents section in your employee detail page.

Go to this article for more details about how to generate your P60s.

Other things to remember

Your employees need to be given a P60 before May 31st - download them after you've ran your last payrun!

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