How to pay employees in a small business

If you don’t pay your staff properly, you won’t have a business for long. Discover how to make sure you’re operating legally, and avoid an unexpected visit from the taxman.

Our experts

We are a team of writers, experimenters and researchers providing you with the best advice with zero bias or partiality.
Written and reviewed by:
Helena Young
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Paying your staff correctly is your legal responsibility as a business owner – meaning it’s really important to get it right. We recommend either choosing quality payroll software, or outsourcing payroll responsibilities to a specialist payroll service provider.

Startups has been working with SMEs for almost 25 years. Below, we’ve condensed all of our knowledge and expertise, as well as the results from thorough research, into a complete guide to everything you need to know about paying your employees.

By the end, you’ll know how to settle staff salaries quickly and efficiently and avoid costly errors – all while complying with relevant regulations.

Compare Costs on Payroll Solutions

Finding a payroll solution that works for your business can be crucial to ensuring high employee satisfaction and smooth business operations. Using our simple, free comparison tool, you can easily compare costs on payroll services for your business. It takes moments, and can help you find the best value solution.

How to do payroll yourself

Payroll DIY in five simple steps: 

1. Register online as an employer. This can be done through the HM Revenue and Customs (HMRC) website.
2. Choose payroll software. Use this to record employee’s details, calculate pay and deductions, and report to HMRC.
3. Produce payslips for HMRC to collect and keep employee pay records
4. Report employee pay to HMRC to record pay, make deductions and report to HMRC on or before the first payday.
5. Pay HMRC from employee wages to settle the tax and National Insurance you owe.

We’ll go through each stage in more detail, as well as how to calculate employee pay and bonuses, further down this guide.

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How to register as an employer

As soon as you decide to hire employee, your responsibilities change. You should register yourself as an employer with HMRC up to one month before you pay your new hire.

Be aware that this process can take up to two weeks, and you can’t register more than two months before you start paying your new staff.

You’re only exempt from registering if you employ workers who earn:

  • Less than £118 a week
  • Less than £511 a month
  • Less than £6,136 a year

If any of these workers receive a pay rise, have an existing pension, are employed elsewhere, or start to receive expenses, you’ll need to register as an employer.

Most limited companies can register online with HMRC in just a few simple steps. Get started by going to the employer registration page. Once done, you’ll automatically be given a login for PAYE Online.

Did you know?

It’s important to note that you should register yourself as an employer if you’re ‘employing yourself’, e.g. as the sole director of your business.

How to calculate employee pay

Calculating the amount of money to offer during the interview stage is a delicate process. The key is finding a good balance between what’s best for the company, and what’s best for the candidates.

The following factors can help you gauge the right salary to offer a candidate.

  • Affordability – This has to be the starting point. Carefully consider the gap this person will fill, how valuable it is to your business, and what impact the expense will likely have on your business’ bottom line.
  • Evaluate the position – Does the role require specialist knowledge or technical training? How much responsibility will they have to make decisions that affect the business?
  • Experience of candidate – Is the candidate a graduate fresh out of university? Or do they have years of experience, or a specialist degree?
  • Industry benchmarking – Many professional bodies publish regular pay surveys, providing a benchmark upon which to base salary scales. The main findings are freely available online.

Our full guide on how much you should pay your staff has more guidance on working out salary benchmarks. To work out how to set your own salary, read our guide to paying yourself as a business owner.

Industry benchmarking

Industry benchmarking is a fancy way of saying that you need to work out how much people in similar roles are being paid in other companies, so you know the going rate for that role.

Remember that these benchmarks are relative to your industry and company size – there is no one benchmark for all roles.

One of the easiest approaches is to use online tools like LinkedIn Salary. Using this tool is very straightforward – start by submitting your own salary details, and you’ll be granted access for a year (details of your salary are kept private). For example, to hire a receptionist in London, enter that info and you get this:

LinkedIn industry benchmarking overview

You can immediately see that the average salary for a receptionist in London is £21,000 a year, while the range is from £16,400 – £27,000 a year. Scroll down the subsequent page and you’ll be given more detailed information, including insight into annual bonuses, commission, and tips.

Salary benchmarking tools like LinkedIn Salary insights are not 100% accurate (they are reliant on information provided by employees and salary levels included in job advertisements), but they should give you a decent idea of what candidates will expect from different roles.


  • Interviewee expectations – Ask your interviewee what they’d expect to be paid (including overtime) – this will help you manage expectations, and ensure that both sides are on the same page.
  • Equal pay – Under UK law, you are not allowed to pay employees a different salary purely based on their sex/gender, race, religion, sexual orientation, or whether they have a disability.
Expert comment

As Head of Talent at MVF Global, Henry O’Justus is an expert in recruitment and compensation negotiation. He advises that salary benchmarks “are not kept static – they need constant review and revision to make sure you stay in line with the market.”

O’Justus offers that the following five pillars are crucial when small businesses are trying to hire talented candidates:

  • Culture – Small businesses tend to have a strong organisational culture. Make sure that this is a key point of your offer and job description, so that candidates feel that this is a special place to work, and somewhere that offers opportunities not readily available elsewhere.
  • Mission & Vision – Studies have shown that Gen Z, the future workforce, are the first age group to put purpose over profit when deciding where to work. Promote your mission statement and company values. They will be much more inclined to work for a company that shares their personal values.
  • Growth & Progression – Startups tend to grow faster and therefore have greater career progression opportunities. Promote this to candidates to reassure them that their starting salary will improve over time.
  • Soft Benefits & Perks – Make sure that you communicate any additional employee benefits or bonus schemes to prospective employees (and be aware the benefits-in-kind require additional HMRC reporting). In today’s economy, with real wages falling, these can help to retain staff when you can’t afford to offer a salary increase.

How many employees will your business have?

Finding the right payroll software depends on several unique factors, including company size. Spend 3 minutes answering some questions about your business’s needs and receive bespoke quotes for payroll software and services.

How to choose a payroll software provider

We’ve put together this comparison table of the top payroll software providers available, based on thorough market research and analysis.

Swipe right to see more
0 out of 0

Sage Payroll




Clear Books



Best for

Small businesses wanting to seamlessly integrate payroll with its accounting software

Best for

Small businesses wanting a comprehensive suite of accounting tools

Best for

SMEs needing extra customer support, and a thorough onboarding process

Best for

Teams with complex payroll requirements, like hospitality

Best for

Micro businesses that want flexible payment plans

Best for

Small businesses wanting to save time by automating payroll processes


£1-7/mo plans
+ 0.40/mo for payroll features


£8/m for 1-5 employees
£13/m for 6-10 employees
£19 – £106/m for additional employees


Provides personalised quotes after assessing business needs


Provides personalised quotes after assessing business needs


£5.40 per month (billed annually)


£5/m for 5 people
£49/m for 10 people
+ £1/m for additional employees

HMRC compliant
HMRC compliant
HMRC compliant
HMRC compliant
HMRC compliant
HMRC compliant

How to pay staff and calculate deductions

Depending on the type of business you own, or what sort of role you’re recruiting for, there are many different types of pay which you may wish to consider offering potential employees.*

Type of PayDescription
SalaryStaff are paid based on the number of hours they would work in a year.
Hourly rateStaff are paid for a set number of hours they’ll work in any given week.
CommissionMost common in sales and recruitment roles, employees receive a share of the sales they make. While commission roles often include a basic salary/wage, this is not always the case.
Piece workEmployees are paid a set amount for every unit they produce – common in the manufacturing and textiles sector.
TipsTips received from a customer directly, such as in a restaurant, do not form part of the employee's pay, as they are the property of the employee and are not paid by the employer. However, you can treat tips to your staff as normal pay if they’re paid into your till – this includes tips added to your customers’ card or cheque payments.

*Always remember, the type of pay you’ll be offering any given staff member should be explicitly stated in their contract of employment.

How to pay freelancers and self-employed staff

Freelancer, self-employed or contract workers take care of their own national insurance contributions (sometimes through an umbrella payroll company), and do not need to be enrolled in the company pension scheme – meaning there are fewer costs for your business to manage. They also don’t have entitlement to sick pay, and can be used more flexibly than full-time staff members. Do note, there are some different rules and regulations for contractors which you will need to be aware of.

Your pay arrangements will depend on the individual freelancer. You may agree to track hours worked on the project using an online system, or you may simply pay them per piece of work produced.

Digital payment platforms like PayPal are popular but not available in certain countries, while a bank transfer is almost universally available but can take days to arrive.

Whatever structure you decide on, make sure you draw up a contract that sets out exactly what is expected from both the company and the freelancer, and that protects you in the event they do not deliver the agreed work.

Additional pay

As well as their normal salary or wages, you may also need to pay employees (and thus record details of) a number of other types of pay, like:


There are three legally-required deductions you’ll need to work out for all employees:

  • Income tax
  • National Insurance
  • Pension contributions

Other deductions that may apply include:

  • Student loan repayments
  • Payroll Giving donations
  • Child maintenance payments

To make deductions for tax and national insurance, you’ll need each employee’s tax code and National Insurance category letter.

Finding your new employee’s tax code

To work out your new employee’s tax code, use the tax code calculator.

For most employees, the information you need should be on the P45 form they received when they left their previous job or stopped claiming jobseeker’s allowance, so make sure to request this before your new employee starts. If this doesn’t apply, then they’ll need to complete a new starter checklist – you can find a helpful new starter checklist template on this page.

Finding your new employee’s National Insurance letter

Working out what national insurance letter your new hire should have is even more straightforward – simply check the table below and see which criteria apply.

Category LetterEmployee Group
AThe majority of employees; anyone who doesn’t fit into the categories listed below will have a national insurance letter of A.
BMarried women and widows entitled to pay reduced national insurance.
CEmployees over the state pension age.
JEmployees who can defer National Insurance because they’re already paying it in another job.
HApprentices aged under 25.
MEmployees aged under 21.
ZEmployees under 21 who can defer National Insurance because they’re already paying it in another job.
XEmployees who do not have to pay National Insurance, such as those aged under 16.


All this can be stressful – especially if you’ve got more than a handful of employees. Thankfully, payroll software takes away much of the pain.

Once you’ve entered the correct information, the process of calculating and removing deductions can be automated – saving you time and money. Simply complete the form at the top of the page to compare quotes now.

How to pay commission to sales staff

When considering a pay model for employees, think about what you can afford, what sort of product or service you’re selling, and what sort of culture you want to promote in your organisation.

Setting up a commission structure can seem daunting – especially for entrepreneurs that have no experience in sales. To help, we’re going to take a look at the pros and cons of some common commission models, starting with the ‘salary plus commission’ model.

Base salary plus commission

This is used by companies all over the world in a huge variety of sectors, as it offers a good middle ground between encouraging competition and providing stability that fosters loyalty.

You pay the salesperson a base salary that covers their living costs in poor months, but also allow them to earn commission – a percentage of every sale (usually deducted from the gross profit associated with that sale) that increases their overall earnings.

Employers will need to set the relationship between salary and commission correctly to ensure that your salespeople are properly incentivised, but also feel supported and valued by the company.

The average split is 60:40, with 60% of total pay being base salary and 40% being commission. However, the right split for you will depend on your industry. If you’re selling a technical product that needs to be explained to the customer (such as pharmaceuticals), then you would expect to make a lower volume of sales. In such cases, a less aggressive pay mix may be more appropriate, such as 75:25.

To set the ratio accurately, consider the following factors:

  • The complexity of each sale
  • The amount of autonomy the salesperson has
  • How much experience is necessary
  • How many leads your salespeople works with

There are two other features you may also want to implement in your base salary plus commission model.

Sales accelerators are for when a salesperson exceeds their target. For example, let’s say the salesperson normally gets 40% of the gross profit they generate – once they exceed their target, this percentage could double to 80%, or they could even receive commission that’s equal to 100% of the gross profit they generate above their target.

A cut-off threshold is essentially a way of protecting yourself in poor months. The commission is only paid at a certain level of sales – once the salesperson has made enough to cover their costs (such as their base salary, car allowance, and other expenses) for example. Alternatively, you could pay a reduced rate of commission on sales significantly below the target level (e.g. pay 20% commission instead of 40% if the salesperson makes under 50% of their target).

Commission only

Under a commission only pay structure, salespeople are only paid for the sales they make and have no base salary to fall back on.

This has obvious benefits for the company, as your salespeople take on all the risk – if they fail, you lose very little. However, using this model makes it difficult to predict your expenses and keep control of your budget, as you have only a vague idea of how much you’ll be paying out from month to month. It also encourages a cut-throat sales culture that can foster employee disloyalty.

Base salary only

Employees are not paid any commission for sales they make, and only receive a fixed salary. While this may make it much easier to forecast company budgets over longer periods, such a structure removes the competitive aspect and promise of high financial rewards is the reason a lot of people go into sales in the first place.

On the plus side, such an approach does reduce the stress of your sales employees, and may be the right fit for roles that are less focused on direct selling and more on forging long-term relationships with customers or clients (such as account managers).

Whatever model you choose, make sure it is simple enough to be understood by your sales staff and potential new hires. Everyone needs to be able to easily work out how much money they’re likely to make under your sales pay structure.

How to produce payslips

As an employer, you are legally required to give your staff a payslip on or before their payday.

Whether you send it online on through the post, the payslip must include:

  • The amount paid before any deductions (‘gross’ wages)
  • The amount taken for deductions such as income tax and National Insurance
  • The amount paid after deductions (‘net’ wages)

Here’s an example of a typical UK payslip:

Example payslip


Key things to note include:

  • The tax code (in the top right corner under deductions)
  • The employee’s National Insurance number (in the bottom right corner)
  • The running totals section (bottom left) – This shows how much has been paid by both the employee and employer in various categories, since both the start of employment and the start of the current tax year.

The easiest way to create payslips is through your payroll software. To discover your perfect fit, simply complete the cost comparison form at the top of the page to compare bespoke quotes from a range of top payroll providers.

How to report employee pay to HMRC

Every payday, you’ll need to send a Full Payment Submission (FPS) to tell HMRC what you’ve paid your employees and what deductions you’ve made.

An FPS has to be sent on or before your employees’ payday, even if you pay HMRC quarterly instead of monthly.

Sample FPS

Source: Moneysoft

To send an FPS, you’ll need to enter the following information into your payroll software:

  • Employer registration details (such as a PAYE reference or Accounts Office Reference)
  • Personal details for each employee listed (Name, address, National Insurance number, date of birth, gender etc.)
  • Employment information for each employee listed (starter and leaver information, whether they are a company director)
  • Year-to-date figures for each employee listed (Tax and National Insurance contributions)
  • Figures for the relevant period for each employee listed (including payment date, gross pay, and the amount deducted for National Insurance and tax)

PAYE reference/Accounts Office Reference

These details can be found on the Payslip Booklet you should have received from HMRC when you registered as an employer. An example of this is shown below:

HMRC Payslip booklet

Source: G Tax Blog

If you’re just starting out and can’t yet afford commercial payroll software, you can use HMRC’s Basic PAYE Tools. This has a number of limitations, however – it can’t produce payslips, for example – and should only be used by businesses with fewer than 10 employees.

If you need to, you can also send the FPS early (if your payroll staff are going on holiday, for example). You’ll also need to send a corrected FPS if any information changes, such as if an employee leaves or changes tax code.

You can’t send reports for the new tax year before March.

Quick payroll glossary

HMRC – HMRC stands for Her Majesty’s Revenue and Customs, and is the part of the government that deals with tax collection and other related duties. As an employer, you’ll need to make payments and electronic submissions to HMRC to verify you are operating legally.

FPS – An FPS is a Full Payment Submission. This needs to be sent to HMRC via payroll software every month and should contain details of what employees have been paid, as well as what deductions have been made.

EPS – An EPS is an Employer Payment Summary. This should be sent instead of an FPS if you’ve not paid any employees in a tax month, and in addition to an FPS if you need to reclaim payments for maternity/adoption or parental leave, or if you need to claim certain tax reliefs. For more information, see the EPS submissions page.

PAYE – PAYE stands for Pay As You Earn, and is the system whereby the employer deducts the tax and national insurance from the wages paid to the employee, and then pays these amounts to HMRC on behalf of the employee. It is the standard system for payroll in the UK.

RTI – RTI stands for Real Time Information, and simply refers to how pay and tax data is now submitted on an ongoing basis. Prior to 2012, employers needed to send various forms to HMRC at the end of every tax year, and every time an employee started or left a job.

How to pay HMRC from employee wages

You are legally required to pay HMRC all of the deductions from employee wages every month.

These deductions will always include tax and national insurance, but may also include other payments, such as child maintenance or student loan repayments.

How to pay your employees

The page on Paying PAYE clearly sets out all the ways you can pay your PAYE bill, and guides you through the process. There are a range of options available, including:

  • Firect debit
  • Debit
  • Corporate credit card
  • Bank transfer
  • The government’s Faster Payments service
  • In person at a bank/building society
  • By cheque through the post

For electronic payments, payment must be made by the 22nd of the next tax month if you pay monthly, or by the 22nd after the end of the quarter if you pay quarterly. If you pay by cheque through the post, then the deadline is the 19th of the month.

What happens if I'm late?

It’s really important to meet these deadlines – if you miss them, HMRC can charge you interest of 3.25% (at time of writing) per day until you pay the amount owed.

If you’re routinely paying less than £1,500 per month, you might be able to pay quarterly instead, so make sure you contact HMRC if this is the case.

Unsurprisingly, good payroll software makes this whole process much easier – you’ll know exactly how much you need to pay, and can quickly pay HMRC. Complete the form at the top of the page to compare top payroll providers now.

How to report employee changes to HMRC

The business world moves rapidly, and employee information changes frequently – and once again, you have a legal responsibility to inform HMRC of these changes.

If any employee details change, you need to send details of new and updated information to HMRC via the Full Payment Submission form discussed above. Inform HMRC if an employee:

  • Joins
  • Leaves
  • Takes a leave of absence
  • Starts receiving a workplace pension/joins or leaves a contracted out pension
  • Changes their home address
  • Becomes a director of your business
  • Reaches State Pension age
  • Goes to work abroad
  • Goes on jury service
  • Dies
  • Turns 16
  • Is called up as a reservist
  • Changes gender

How to change payday

To change your payday to a different day: simply treat the first new payment as an extra payment for that period.

To pay your employees less often (e.g. if you want to switch from paying weekly to paying monthly): contact HMRC to avoid being charged a non-filing penalty.

If the new payday is in a different tax month or week, you do not need to do anything special when recording pay.

If you need help working out National Insurance after you’ve changed payday, refer to this guidance on aligning payroll to the correct tax period.

Most payroll software can make it easy to change your payday, automatically working out the correct deductions and saving you a massive headache. Complete the form at the top of the page to find the right fit for your business.

How payroll services and software can help you: a summary

As is covered in this article, payroll software and services can help small business owners with:

  • Deductions and tracking: easily work out deductions and keep track of the different ways your staff are paid
  • Payslips: automatically produce payslips every payday
  • FPS: send pay data to HMRC with the click of a button
  • PAYE/HMRC payments: instantly know exactly how much you need to pay HMRC every month, and avoid being fined for late or inaccurate payments
  • Changing payday and National Insurance: change payday whenever you need to, and have the new National Insurance contributions worked out automatically

Payroll software and services can also allow your business to:

  • Get live business updates with integrated HR
  • Securely store your data
  • Cut down on paper with online payslips
  • Have an experienced professional at your service if you need any help

These benefits mean that finding the right payroll partner can transform your business and save you time and money.

Use our simple cost comparion tool to get bespoke quotes from a range of top payment providers and take the first step to making your business more efficient, more profitable, and more successful.

Small business payroll FAQs
  • What if I make payroll mistakes?
    If you make a mistake with your payroll, a lot of providers (like Sage) have a built-in corrections feature allows you to amend data without rerunning pay runs. Be wary that the process is more complicated with other providers, like Xero, which require you to post an unscheduled pay run to correct the mistake quickly, and file it with STP.
  • Can I do payroll without software?
    No. Working your employee salaries out with a pen and paper will take countless hours and is also much more likely to lead to errors. Payroll software automates the whole process for you, which is why it's a critical tool for running a business.
  • Can I do payroll without an accountant or payroll service?
    Yes! It is perfectly possible to DIY your payroll by using a HMRC-recognised payroll software, like Sage. UK business owners can use these to set up tax, PAYE and NI for your business effortlessly.
  • How do you do simple payroll?
    Payroll software is the simplest way to do payroll. All you need to do is register as an employer with HM Revenue and Customs (HMRC), and then choose a payroll softare from the government approved list to record employee’s details, calculate pay and deductions, and report to HMRC.
  • Can I do PAYE myself?
    Yes. Once you have registered as an employer with HM Revenue and Customs (HMRC) and get a login for PAYE Online. is reader-supported. If you make a purchase through the links on our site, we may earn a commission from the retailers of the products we have reviewed. This helps to provide free reviews for our readers. It has no additional cost to you, and never affects the editorial independence of our reviews.

Written by:
Helena Young
Helena is Lead Writer at Startups. As resident people and premises expert, she's an authority on topics such as business energy, office and coworking spaces, and project management software. With a background in PR and marketing, Helena also manages the Startups 100 Index and is passionate about giving early-stage startups a platform to boost their brands. From interviewing Wetherspoon's boss Tim Martin to spotting data-led working from home trends, her insight has been featured by major trade publications including the ICAEW, and news outlets like the BBC, ITV News, Daily Express, and HuffPost UK.
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