By Ashley Preen

May 4, 2022

What Are the Best Payroll Systems in the UK?

If you have employees then, by law, you need to “run payroll” every time you pay those employees. So, if you pay employees every week, then you need to run payroll every week. (And if you pay them daily then you would need to run it daily!)

Payroll is a complicated task that used to take an enormous amount of time to complete before the advent of sophisticated payroll software.

As the old saying goes, “One man’s meat is another man’s poison”, and determining the “best” payroll software for your company is as much a matter of choice as it is a matter of budget and features.

So, instead of telling you outright which of payroll software is “the best” for your company, we’ve listed software and tools we believe to be an excellent choice for any company, depending on their personal preferences and circumstances.

1. Xero payroll functions

If you’re already using Xero, then the natural choice might be to use Xero Payroll to manage your payroll.

Xero Payroll takes care of all the necessities with running payroll, providing automatic calculations, pension deductions and even providing employees with e-payslips which they can access on their computers or mobile phones.

Xero Payroll allows you to create P45 and P60 forms as needed, and your employees can also submit their timesheets directly to Xero.

2. Quickbooks and payroll

For those of you already using Quickbooks for your accounting, then using Quickbooks Payroll might be the simplest solution. Employees can access their payslips directly within Quickbooks, from any device, and their personal data is stored in a GDPR-compliant manner.

Both the standard and advanced payroll add-ons come with automatic pension deductions and a suite of features for making payroll a breeze.

3. Brightpay

Brightpay is an award-winning payroll software which, unlike the two cloud offerings above, is installed on a desktop computer.

The software is recognised by HMRC as meeting the required standards for running payroll. It also connects seamlessly with Quickbooks, Xero and FreeAgent so that you don’t have to be stuck with one platform for this additional accounting feature.

Last but not least, Pearl Accountants is an official partner with Brightpay (we are also partnered with Quickbooks, Xero and FreeAgent) so we will be able to help you with any difficulties you might run up against when using this tool to do your payrolls.

4. FreeAgent

FreeAgent Accountants

FreeAgent is a popular accounting tool for small businesses, freelancers and sole traders. It also comes with payroll “baked in” as part of its package, as opposed to needing to purchase an additional module or add-on to set up payroll.

FreeAgent prides itself in its simplicity so that anybody can use it, and its payroll features are no different. Their extensive help articles assist even those laypeople among us to feel like veteran accountants. Oh, and their friendly support is top-notch.

5. Sage Payroll

Sage offers a sophisticated cloud-based payroll solution for SMEs.

The company boasts a simple “four-step” payroll run to take the headache out of running payroll. It includes all the usual features of HMRC-approved payroll software: Pension filing, P60-form generation, payslips and reporting.

The cost of adding payroll to your Sage package depends on the number of employees you have.

6. KashFlow Payroll

KashFlow is accounting software aimed at small businesses. Their cloud-based software offers bookkeeping, invoicing, expense management and, as part of a separate module, payroll.

Of course, their payroll module integrates fully with their bookkeeping service so that there’s no need to manually input bookkeeping changes once the payroll has been run. Employees can access their payslips digitally from any device, which saves time (and paper!).

The submission of P60 and P11D forms are automated.


MyPAYE is a dedicated payroll software which specialises in Workplace Pensions and Auto-Enrollment. It is extremely affordable — just £1 per employee as of this writing — and integrates numerous accounting systems, including:

  • Xero
  • Quickbooks
  • KashFlow
  • And others

It is a simple “no-frills” package which gets the job done efficiently and cost-effectively.

8. Payroo

Payroo offers free payroll software for small businesses with less than ten employees. If you have ten or more employees, the fee is only £3 per annum!

The tool is approved by HMRC and, incidentally, also offers a MTD VAT mobile app for users.

Payroo offers all the essential features that the “big shots” also offer — P11D and P60 submissions, reports, etc.

Unfortunately, from what we could see, Payroo does not integrate easily with external accounting tools.

So, which one?

Choosing “the best” payroll software for your company depends on:

  • Your budget
  • Your company’s size
  • How much time you want to save
  • What tool(s) you’re already using.

That you’re using, say, Xero, doesn’t automatically mean you have to use the Xero Payroll feature.

Choosing “the best” payroll software for your company depends on

You could as easily go with something like Brightpay if you found that their service or pricing was better value for money.

Ease-of-use is another crucial matter to consider when choosing the right payroll software. The point of using accounting and payroll software is to save time and reduce complexity, not add to it.

But of the tools mentioned above is indeed “best in its class” and we would recommend any of them if it suits your business’s needs.