Choosing a payroll system

Managing payroll is a key task for any employer. It involves paying your employees correctly, making deductions for tax and National Insurance contributions (NICs) and keeping proper records of all this.

You can handle payroll in-house, or you can outsource it. If operating payroll in-house, there are significant advantages to using electronic payroll software rather than manual methods. Using software saves time, reduces errors and makes many of your payroll tasks much easier to complete. It's a particularly good choice now that online filing of the Employer Annual Return and in-year starter and leaver forms is a requirement for almost all employers.

This guide aims to help you make the right choice when you choose a payroll system, whether you're a new employer wondering where to begin or are considering changing from paper to electronic payroll, or from in-house to outsourcing.

On this page:

What is payroll?

'Payroll' refers to the records - paper or electronic - and calculations that you make to work out your employees' pay and deductions under the Pay As You Earn (PAYE) system. It covers all the payments you make to your employees, including:

  • wages and salaries
  • overtime
  • commission and bonuses
  • holiday pay
  • statutory payments - Statutory Sick Pay and Statutory Maternity, Paternity or Adoption pay

Payroll covers things like employers' NICs and the value of perks and benefits too. It also shows all the deductions you make before paying your employees, like Income Tax, employees' NICs and any student loan deductions.

It's essential to your business that you pay your employees the right amount and on time - and that you make the correct deductions. So keeping accurate payroll records is really important.

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Your payroll options

You have three main options:

  • outsource your payroll - you can pay an accountant or a specialist agency to look after all the necessary calculations and record-keeping
  • in-house electronic payroll - you use specialised payroll software to store employee records on a computer and calculate PAYE and NICs automatically
  • in-house manual payroll - you keep written records of each employee's details, and calculate PAYE and NICs yourself

Whichever method you choose, you'll need the figures from your payroll records to complete and file your in-year starter and leaver forms (P45 and P46) and your Employer Annual Return (P14s and P35). Almost all employers are now required to file these forms online, so there are big advantages to maintaining your records in an electronic format throughout the year. Most commercial software will seamlessly transfer the figures from your payroll records into these forms and then allow you to file online automatically. HMRC’s free P11 Calculator will do this for forms P45 and P46 and for your annual return, provided you have no more than nine employees at the end of the tax year.

If you outsource your payroll, it's important to note that you're still legally responsible for deducting the correct amount of tax and NICs and for paying it over to HMRC.

Filing your Employer Annual Return online: P35 and P14s

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Outsourcing payroll - options and considerations

There are many providers that can offer you an outsourced payroll service. Most accountants offer a payroll service. Some may even run a specific department that deals just with this.

It might make business sense to ask your accountant if they can provide you with payroll services. They'll already be familiar with your business and might offer you a competitive rate as part of a package of services. Alternatively, you could outsource your payroll to a payroll agency.

Either way, you can normally specify the level of involvement you want from them. For example, you may choose to completely outsource your payroll or you may simply wish them to provide you with your weekly/monthly payslips.

However, before handing over your payroll operations, you need to consider:

  • whether the service provider can tailor a suitable package
  • whether they're experienced with your type and size of business
  • whether they can supply weekly/monthly payslips, and provide weekly, monthly and annual returns
  • the charge for setting up the payroll system
  • the charge for administering the system
  • whether the fees include making all the types of deductions
  • whether they charge any additional fees
  • how easily scalable their service is - eg, if you take on another employee
  • what software they use - whether it's HMRC accredited, whether it's compatible with software you use, and whether it keeps your records in a format that will allow for easy online filing (of forms P14, P35, P45 and P46)

Checklist - using an outsourced payroll supplier

Outsourcing your payroll to a third party will generate another overhead for your business. However, you might feel this cost is justified by the time and money that is saved through reduced administration costs and paperwork. Outsourcing your payroll can also make savings by:

  • allowing you to concentrate on other areas of business
  • reducing employee overheads as you'll no longer need to employ a payroll specialist
  • improving the accuracy of your systems as they're likely to be computerised

However, to reap these benefits you need to make sure that any contract you agree with an outsourced payroll supplier is written carefully. Make sure that you:

  • specify that they'll calculate tax and deductions accurately, given the information supplied
  • state that they'll make these deductions to your specific timescales
  • agree that they'll ensure mandatory requirements are completed or met within the regulatory timescale required
  • stipulate that in the event of their failing to comply with these requirements, provision is made for them to reimburse you for any resulting penalties
  • specify that they'll keep the necessary records of any taxes and deductions as required by HMRC
  • spell out that any additional payroll charges you might incur should be specified
  • specify that some provision is put in place for any future expansion of their service

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Operating in-house payroll using commercial software

A computerised payroll will almost certainly be more convenient and less time consuming to operate than carrying out manual calculations, particularly if you're going to employ a number of people.

What will commercial payroll software do?

You'll have to record the employee's details initially, using information from the form P45 or form P46. However, once you've done this, the software will:

  • calculate Income Tax, NICs and student loan deductions every payday
  • calculate the NICs you have to pay as an employer
  • produce pay statements for your employees
  • keep records of payments and deductions

The software will also produce the figures you'll need at the end of the tax year, and help you deal with other payroll related events, for example if an employee leaves.

Your software provider will send updates as and when necessary - for example, if a tax rate changes following the Budget. Make sure you install these updates so that all calculations are carried out correctly.

Read more about commercial software supplier products

Online filing

Many software packages also make it easy to file your in-year starter and leaver forms and your Employer Annual Return online. They automatically transfer the necessary figures from your payroll records to these forms, which are then sent direct to HMRC over the internet.

Almost all employers are required to file these forms (P14, P35, P45 and P46) online rather than using paper forms.

Filing your PAYE in-year forms online: P45, P46 etc

Filing your Employer Annual Return online: P35 and P14s

Help with choosing a commercial software package

HMRC strongly recommends choosing commercial payroll software that meets the criteria it has set for the Payroll Standard accreditation scheme or the PAYE Recognition Scheme.

List of payroll software within the HMRC PAYE Recognition Scheme

List of HMRC-accredited payroll software products and suppliers

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Operating in-house payroll using free HMRC software

As an alternative to commercial software (some of which is free) you can manage your payroll using HMRC's free P11 Calculator. This doesn't offer a complete payroll system but it will work out your employees' deductions for you.

The P11 Calculator also provides many employers with a simple way of meeting the requirements to file in-year starter and leaver forms and their Employer Annual Return online.

You can file your starter and leaver forms online directly from the P11 Calculator. And if you have up to and including nine employees on the last day of the tax year (5 April), the calculator will also:

  • use the figures from your payroll records to complete your annual return automatically
  • connect you to HMRC and file your return online

Check the features and limitations of the P11 Calculator

Filing your PAYE in-year forms online: P45, P46 etc

Filing your Employer Annual Return online: P35 and P14s

Where to get HMRC's free P11 Calculator

A set of Basic PAYE Tools are now available to download straight to your computer. In addition to the P11 Calculator, the tools include:

  • an employer database on which you can record your employees' details
  • a range of other calculators that work out, for example, statutory payments
  • interactive forms such as P11D working sheets
  • a Learning Zone - including interactive material on how to use the Basic PAYE Tools

Download Basic PAYE Tools from the Business Link website (Opens new window)

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Operating in-house payroll manually

Whereas payroll software automatically works out payments and deductions and then updates your payroll records for you, with the manual method you use either calculators or tables to work out the figures and update your records yourself. This is a more time-consuming way of managing your payroll than using software.

It also creates additional work for you when an employee starts or leaves your business and at the end of the tax year now that online filing of in-year starter and leaver forms and of the Employer Annual Return is a requirement for almost all employers. Even if you keep manual payroll records throughout the tax year, you'll still need to transfer key details into a format that can be filed online at the end of the year. A simpler option is keep your payroll records in an electronic format that's ready for online filing from the start of the year.

What you need

To get started, HMRC recommend you download helpbook P49 'Paying someone for the first time'. You can find this and other helpbooks, as well as tax tables and other support for manual payroll in our guide 'Forms and publications for employers'.

If exceptionally you are unable to download the forms and guidance, telephone HMRC's Employer Orderline.

If you need more help, you can read the guide 'New employer - getting started' on the Business Link website.

Forms and publications for employers

Download helpbook P49 'Paying someone for the first time' (PDF 5.6MB)

Find contact details for HMRC's Employer Helpline

Find contact details for HMRC's Employer Orderline

New employer - getting started on the Business Link website (Opens new window)

Download HMRC's Basic PAYE Tools from the Business Link website (Opens new window)

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More useful links

Guidance for exempt employers: filing your PAYE forms on paper

Find interactive e-learning on setting up a payroll system on the Business Link website (Opens new window)

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