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Best Paye Software for Small Business

Payroll software for small business and start up is designed to handle all of the complex and minute details that go into calculating payroll for your business, regardless of the size of your company and the number of employees you have. The only downside with using business payroll software is the cost, which can be quite high. If you are a small business or startup, however, you may be unable to afford the cost of business accounting payroll software.

Computers have altered the whole idea of companies and organizations. Like every other thing man means to do, computers have also made a huge impact on how business companies handle their payrolls. Payroll is an important requirement for any given company as this is where employees are paid for their work. With the advent of new computer software, small companies are becoming competitive with their larger counterparts in terms of producing professional payrolls

Choosing a payroll software for your business can be a daunting task, due to the sheer amount of options available. In this article, I talk about the three different kinds of software that are currently offered and provide my personal opinion on what is the best option for a small business.

If you are looking for a payroll software for limited company, corporation, or other business entities, we can help. Our software will provide businesses like yours with quick setup and easy to use. This includes managing hourly and commission-based employees. It’s our goal to make your payroll process as simple as possible. Learn more about us here today!

What is payroll software?

If you’re running a business with employees in most cases you’ll need payroll software. Payroll software will enable you to carry out the following tasks:

  • Calculate and deduct PAYE contributions for your employees.
  • Send Full Payment Submission (FPS) reports to HMRC.
  • Create and distribute payslips.

The alternative to using payroll software yourself is to appoint someone else to do it for you. For example, you may choose to save time and effort and pay for an accountant or payroll firm to do it for you. 


Founded in 2006 in New Zealand where it’s still headquartered, Xero is very well known for its cloud-based accounting software. Xero Payroll “not only manages the tasks you have to do, it automatically updates your accounts and creates HMRC submissions, too”. It’s marketed as payroll software that offers “all the tools you need”.


Free for your first three months with any Business Edition plan. Thereafter, £5 for up to five payroll employees per month, + £1 for each additional employee a month, to a max of 200.  

Key selling points:

  • “Makes it easy to track employee time and leave, process pay and pensions and report the right information to HMRC”.
  • Easy to make adjustments.
  • Automatic tax and leave calculations, with accounts also updated.
  • Simple RTI submissions to HMRC.
  • Securely accessible from any device.
  • Easy to customise and designed to save business owners time.
  • Employees can use the app to provide timesheets or request holiday leave.
  • 30-day free trial.


Xero has an extensive portal called Central that features guidance on a wide range of accounting and payroll subjects. Xero also provides unlimited free 24/7 online support to subscribers.


Developed and marketed by Intuit, the company founded in California in 1983, cloud-based accounting software QuickBooks is used by millions of small businesses throughout the world.

With the Quickbooks’ payroll add-on you can: “Save time with our smart payroll software and focus on what matters most”. You can “Sort payslips, pensions and statutory pay, then make real-time submissions to HMRC from any location.”


Payroll is an add-on to QuickBooks. There is a standard version priced at

£4 a month +£1 per paid employee or an advanced solution for £8 a month + £1 per paid employee a month. Both must be combined with a QuickBooks subscription (£5-£12 per month for a six-month subscription).

Key selling points:

  • Simple to use. Mac or Windows.
  • Free QuickBooks app available.
  • You can make multiple pay schedules, weekly and monthly.
  • Easy to make statutory maternity, paternity and sick leave payments.
  • Net pay, taxes and NICs and pension contributions are all calculated.
  • Simple to easy to enter and make overtime/bonus payments.
  • Payslips can be printed or emailed to staff.
  • RTI data sent automatically to HMRC.
  • Workplace pension/auto-enrolment assessment and calculation of pension contributions.
  • Automatic update of tax codes at the start of the tax year.
  • “Journals automatically created and posted to your QuickBooks account”.


Intuit publishes much user information online. Free technical support is also available via Intuit’s messaging or call-me-back facility.

Sage Payroll

According to Sage, half of all businesses in the UK use Sage Payroll, which it describes as: “The UK’s most trusted payroll solution”. And when you use it you become “part of a big club: from start-ups to household names, thousands of businesses trust Sage payroll solutions”.

Sage offers dedicated payroll solutions for businesses with fewer than 25 employees, more than 25 employees and accountants that offer payroll services.


Get three months free, then £7 +VAT per month for up to five employees (£12 +VAT a month for up to 10 employees; £17+VAT a month for up to 15 employees and £27+VAT a month for up to 25 employees – all with three months free initial offer). 

Key selling points:

  • Easy to use yet comprehensive web-based solution.
  • Available as a standalone solution.
  • Alternatively, integrates with Sage accounting software.
  • Print or email your payslips, P60s and reports.
  • Easy to amend previous pay runs; adjustments are handled automatically.
  • Seamless integration with pension providers.
  • Free trial. You can also get Sage payroll free for three months, when you sign up. No commitment, cancel anytime.


You can communicate with Sage’s UK-based team over the phone, by email or live chat. Sage also has an online help centre.


The best HR outsourcing service



+Comprehensive features+Self-service platform+Fortune 500 benefits

Oasis is a Paychex-owned Professional Employer Organization (PEO) and provides a full range of full HR solutions for business, to cover the entire employee lifecycle, including of course Payroll.

This means covering everything from recruitment to onboarding, payroll and benefits, as well as development and training. Oasis also ensures regulatory compliance and mitigating risk.

Oasis does this through a combination of self-service computer software for easier employee management, to personalized support to ensure you’re getting the help you need.

Performance management also ensures that employee development works in line with your business strategy.

Because Oasis is part of Paychex, which has offices across the US, the company can offer competitive benefits and insurance packages for employees on a par with those offered by Fortune 500 companies.


Best dependable payroll solution



+Easy to use +Works out tax +Full-service payroll in all 50 states


-Less suited to big firms-Efficiency could be better

Gusto offers a full-service payroll, incorporating time tracking, compliance, as well as managing taxes, 401(k), and benefits such as medical, dental, and vision plans. 

Gusto also integrates with a number of existing accounting software and related platforms, such as Freshbooks, Quickbooks, Aplos, Zipbooks and Xero accounting software.

There are a handful of different plan levels available, with the cheapest offering to cover the basics of payroll, by way of a monthly software fee plus a fee per employee. After that plans offer features such as onboarding, time tracking, accounting, benefits, and document management. 

There is also a full-service payroll available, which along with employee self-service, also offers onboarding, directories, surveys, as well as support and a resource center.

PrimePayroll – Easy. Flexible. Compliant Payroll

PrimePayroll is an enterprise cloud service for payroll and human resource management. Many small business owners and organizations still face payroll management and HR challenges in the day-to-day administration of their business. In addition, the upfront cost implication of purchasing and setting up legacy payroll systems, together with the required infrastructure setup can be prohibitive and financially be tasking.

PrimePayroll takes care of your payroll and HR administration, giving you the freedom and flexibility required to grow your business. PrimePayroll is safe, efficient and simple to use with zero upfront investments, all from the comfort of your internet-enabled PC or mobile device.

Intuit Payroll

Intuit payroll software is a UK platform that will give you peace of mind and a happy workforce all while saving you time and money. This software tool offers you access to powerful features such as; HMRC submissions, payslip printing, CIS, automatic enrolment, video support amongst many others. Full review

  • •Video call support
  • •Quick and easy set up
  • •Affordable

QuickBooks Payroll

What We Like

  • Seamlessly integrates with QuickBooks accounting software
  • Same- and next-day direct deposits
  • Unlimited pay runs with automated payroll tax filings (federal and state)
  • Mobile app lets you run payroll and e-file taxes even while on the go

  • Automated local tax filings available only in higher tiers
  • Lacks a contractor-only plan
  • Basic HR features
  • Doesn’t have mobile apps for employee self-service (only offers a workforce portal you can access online)

QuickBooks Payroll Pricing

  • Core: $45 per month + $4 per employee monthly
    • Includes full-service payroll, next day direct deposit, federal and state tax filings and payments, and access to 401(k) plans and benefits*
  • Premium: $75 per month + $8 per employee monthly
    • Everything in Core plus same-day direct deposit, federal, state and local tax payments and filings, workers’ compensation administration, and HR support center
  • Elite: $125 per month + $10 per employee monthly
    • Everything in Premium plus multiple state tax filing, project tracking, personal HR adviser, tax penalty protection up to 25k per year, and expert setup

*Additional fees may apply depending on the selected plan.

QuickBooks Payroll is the best option for most QuickBooks accounting users. It integrates seamlessly—you access it within the same system with the click of a button—and all information flows throughout both systems (you don’t have to enter twice).

Like Gusto, it offers full-service payroll with automated tax filings (federal and state, local taxes if subscribed to the Elite plan), year-end reporting (W-2s and 1099s), and an online portal where employees can access their pay stubs, tax forms, and PTO balances. It also has fast direct deposits; its standard timeline is next-day but has same-day options if you get one of its higher tiers.

In our evaluation, the platform earned a 4.62 out of 5, with perfect scores in ease of use, pricing, and reporting. While all of its other ratings are 4 and above, it scored the lowest in HR features (4.13 out of 5), mainly because it doesn’t file new hire state reports (it only generates them) and you have to get its Premium plan if you want time tracking and expert advice from a personal HR advisor.

However, many users still appreciate its ease of use, especially its seamless integration with QuickBooks accounting. A few others complained about having experienced occasional software glitches, while some said that it can be pricey for small businesses.

QuickBooks Payroll Features

  • Automatic and unlimited payroll: You can approve and set payroll to run automatically with QuickBooks. It also lets you process payroll as many times as your business requires.
  • Automated payroll tax services: Like most of the payroll providers on this list, QuickBooks Payroll handles all tax calculations, payments, and filings (including year-end reporting) for you. However, its tax filing services only cover federal and state taxes. You have to be on an Elite plan if you want automated local tax filings—otherwise, you’ll have to enter the local tax rates yourself.
  • Fast direct deposits: Apart from next-day direct deposits, you can pay employees through same-day direct deposit at no extra cost, provided you subscribe to QuickBooks Payroll’s higher tiers. Note that most of the providers on this list have a standard two-day processing time—although Square Payroll offers instant payments if you have a Square Payments account.
  • Tax penalty protection: QuickBooks will cover the penalty and interest for any payroll tax error for up to $25,000 a year—regardless of who made the mistake. Note that you must purchase its Elite plan to have your errors covered. Experts will also represent you before the IRS and concerned agencies and will assist you to resolve the problem. No other providers on our list will offer to represent you to help fix tax issues or cover mistakes you make under any circumstance.
  • Payroll and tax filing while on the go: With QuickBooks Payroll apps (for iOS and Android), you can process payroll, pay taxes, and e-file tax forms in all 50 states. (It is our top-recommended payroll app.) Square Payroll, ADP Run, and Paychex may let you run employee payroll on its mobile apps, but they don’t have the tax e-filing feature that QuickBooks Payroll offers.

QuickBooks Payroll’s Drawbacks

  • Lacks mobile apps for employee self-service: While QuickBooks Payroll has a workforce portal where employees can check PTO balances, access payslips, and view tax forms, its self-service tool doesn’t have a mobile app version. We recommend either Square Payroll, ADP Run, Homebase Payroll, and Paycor since these providers offer mobile apps for employee self-service. Gusto’s financial management app, Gusto Wallet, also lets you view pay stubs and W-2s but doesn’t show PTO details.
  • Tax penalty protection can be costly: Compared to the other providers in this guide, QuickBooks Payroll offers more robust tax penalty protection for its clients, which includes representing your business before the IRS to help address tax issues. However, coverage for its tax penalty protection is expensive since you have to sign up for its highest tier, Elite, which costs $125 per month plus $10 per employee monthly.

What do I need to do to use payroll software?

In order to run your payroll, you will need to set up your payroll software with the following information:

  • Employer information provided by HMRC
    • PAYE reference number
    • Accounts Office reference number
  • Employee information:
    • Full name
    • National Insurance number
  • Login details for your online PAYE account
    • User ID
    • Password
  • Employee payment information
    • Weekly or monthly pay
    • Hourly rate


A payroll software program can help you manage your small business payroll more efficiently. That can be especially important for small businesses with limited human resources staff. Payroll software also can increase the accuracy of your employee paychecks. You may also find that using payroll software better complies with federal and state regulations

Best payroll software for small business comes with various features and specifications. When looking for the best paye software for small business, it is necessary that you select a real-time software that will help you manage employees’ time

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