6 reasons your business should keep HR and payroll software separate

24 min read  |   21 July, 2025   By Elise Featley

A cheerful, small robot exhales a sigh of relief beside a large speech bubble that reads “WORK SMARTER NOT HARDER” in bold, uppercase letters. The robot, styled in soft teal and blue tones, stands on the left with closed eyes and a content expression, while the speech bubble appears on the right against a deep blue background.
    

If you’re running or scaling a business in the UK, you’re probably all too familiar with the pitfalls of juggling spreadsheets, duplicate data entry, and clunky all-in-one systems that claim to "do it all”, but rarely actually “do it all well”.  

The reality? Manual payroll processes are error-prone, compliance headaches are real, and relying on a single system for everything can leave your business vulnerable.  

That’s why growing businesses choose simple, connected platforms that work better together.  

At Breathe HR, we champion a smarter approach.  

Trying to do everything in one system can get messy. It’s much easier when your HR and payroll tools are built to connect. And when it comes to payroll, our Xero integration is leading the way for UK SMEs and ambitious businesses looking to grow.  

Just as every tool has its purpose, your business is better off using dedicated systems for HR and payroll, each built to do their job well.  

 

1. Integrations are the future

2. Freedom, flexibility and scalability 

3. Designed for growth  

4. Reduced risk using a separate payroll software solution

5. Stay in control

6. Future-proofing: Keeping your options open  

 

What Breathe HR does best

Breathe HR is your go-to HR software for:  

  • Employee self-service  

It’s built for people management, not payroll.  

 

What payroll systems do best  

Dedicated payroll tools, like Xero, excel when it comes to:  

  • PAYE & National Insurance  
  • Statutory pay (SSP, SMP, etc.)  
  • Auto-enrolment pensions  
  • RTI submissions & P60 generation  
  • Payslip distribution & tax compliance  
  • HMRC recognised payroll software  

 

Payroll software takes the stress out of pay runs and payroll processing, helping you manage multiple pay cycles with ease while streamlining admin tasks. Purpose-built for HMRC compliance, they reduce the risk of errors and keep everything running smoothly. 

Think of HR as your people engine, driving culture and performance. Payroll? That’s your compliance gearbox, crucial for staying on track, but built for a different job entirely. 

 

Let’s talk about the best software for payroll  

We believe HR and payroll should stay separate, but seamlessly connected. That’s exactly what we build at Breathe HR.  

Our integration with Xero Payroll is a prime example of this in action, allowing you to streamline onboarding and payroll processes in just a few clicks.  

Here’s how it works:  

  • Automatic data sync: Employee profile information, changes in pay or working pattern? They’re pushed directly to Xero. No double-handling.  
  • Payslips: Once payroll runs in Xero, employees can access their payslips in  Breathe. 
  • Leave and sickness: Absence data in Breathe flows to Xero to ensure accurate pay calculations 
  • Effortless compliance: Xero handles RTI submissions, pension auto-enrolment, and all things HMRC, using accurate, clean data from Breathe.  

The result? Reduced admin, better compliance, happier employees, and a more efficient, connected business.  

 

 

1. Integrations are the future  

Gone are the days when your business had to compromise with an all-in-one system that wasn’t quite right.  

Today’s leading HR and payroll software solutions are designed to work together – automatically, accurately, and without the faff.  

The key benefits of integrating dedicated HR and payroll systems include:

  • Improved accuracy  
  • Enhanced automation  
  • Greater flexibility  
  • Timesaving  

All making payroll management more efficient and reliable.  

Instant updates, no need to retype data  

Employee data, including payroll details, flows directly from Breathe HR into your payroll system.  

New starter? Leaver? Salary change? Thanks to Breathe’s partnership with the UK’s leading payroll software provider Xero, your info goes straight to Xero Payroll, with no need to enter it twice.  

The result? Fewer payroll errors and improved data accuracy.  

Less manual admin = more time for people  

Say goodbye to hours lost in payroll prep.   

Automation helps HR and finance teams save time by streamlining tasks like tax calculations, payslip generation, and HMRC submissions. 

With Breathe HR and Xero, your HR and finance teams save valuable time, easing the administrative burden and freeing them up for more strategic, people-focused work.  

Choose the tools that fit you  

Why settle for a one-size-fits-all solution?   

With integrations, you can tailor your software stack to your business’s exact needs (and budget).   

Use the tools you love, and change them as you grow. Choosing a trusted partner for your payroll and HR integrations ensures reliable support and long-term success as your business evolves.  

 

Breathe product image

 

2. Freedom, flexibility and scalability 

Your business isn’t static, so why should your software be?  

Pairing payroll and HR software gives your business the freedom to grow without being stuck in outdated systems.  

With cloud-based payroll, you can access data anytime, anywhere, whether you're in the office or on the move. That means real-time updates and quick changes when you need them.  

Need to change payroll providers? No problem. Your employee data stays safe and intact in Breathe, while you link to the new payroll solution. No upheaval. No lost history.   

Scalable payroll solutions can also support multiple clients or businesses, making it easier to manage growth and handle several accounts efficiently as your organisation expands.  

Just as every tool has its purpose, your business is better off using dedicated systems for HR and payroll, each built to do their job well.  

 

3. Designed for growth  

Add employees to Breathe HR as you grow, and automatically sync data to your payroll provider.  

As new employees are added and data is synced, employees access their payroll information and payslips through the Breathe HR mobile app.  

Cloud-based payroll software and HR software 

Cloud-based payroll software makes running payroll easier and more flexible. You can process payroll from anywhere, as long as you have an internet connection. 

The same applies to Breathe HR software, it’s cloud-based too, giving you secure access to employee data, records, and workflows from anywhere, whether you're in the office or on the go. 

One big benefit is better data security.  

Top providers use strong encryption, secure servers, and follow strict standards like ISO27001 to keep your payroll data safe. Breathe HR is also ISO27001 accredited, so you can be confident your HR data is protected to the highest standard. 

Many systems also come with a dedicated payroll app. This lets employees quickly check payslips, request leave, and approve timesheets from any device, making payroll faster and more user-friendly. 

Cloud payroll software also works well with workplace pension providers. It can handle automatic pension contributions, send data electronically, and help you stay compliant, all while reducing admin time. 

 

 

4. Reduced risk using a separate payroll software solution  

Relying on one system for everything? That’s a risky game.  

Opting for a separate payroll software solution is a smart way to reduce risk and ensure your payroll processes run smoothly.  

Manual processes and calculations can be time-consuming and are often prone to costly mistakes, which can lead to compliance issues and unwanted penalties.  

By automating payroll calculations and tax deductions, you can achieve accurate payroll every time, giving you peace of mind that your employees are paid correctly and on time.  

A cloud-based payroll solution adds another layer of security, keeping sensitive payroll data protected from unauthorised access or data breaches.  

With dedicated payroll software, your business benefits from real-time insights and comprehensive reporting, making it easier to monitor payroll processes and stay compliant with HMRC regulations.  

Separating your payroll software from HR systems also means you can quickly identify and resolve any issues, without disrupting other business functions.  

Ultimately, a dedicated payroll solution helps your business stay secure, compliant, and efficient, no matter how much you grow.  

 

5. Stay in control  

Avoid vendor lock-in. Some systems try to tie you in for multiple years – it's better not to be tied to one system’s pricing or roadmap.  

With Breathe HR and Xero, you’re free to choose what’s best for your business, every step of the way.  

With Breathe we don’t offer lengthy contracts. Choose a rolling monthly or annual plan -  it’s up to you.  

 

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6. Future-proofing: Keeping your options open  

The future is fast-moving. Regulations change, technology advances, and business and organisation needs evolve.  

Embrace change with ease  

A modular software stack, like Breathe HR and Xero being used together, gives you the flexibility to respond quickly to changes in tax regulations, pay models, or workforce structure.  

Always benefit from innovation  

Xero Payroll and Breathe HR each invest heavily in product development. By keeping them separate, you’re free to adopt the latest advancements in each specialism, without being held back by a slower-moving all-in-one.  

 

Bonus: Additional operational benefits  

Isolated system issues  

If your HR software crashes, you still need to pay your team. If your payroll has a hiccup, you still need access to employee records. Separate systems ensure business continuity.  

Easier troubleshooting  

Is it a payroll problem or a data input error? Segregated systems help you quickly isolate and solve issues.  

Safer data handling  

Store sensitive payroll information, like salaries and bank details, securely in Xero Payroll, a system built for financial compliance and data protection.  

Meanwhile, Breathe HR safely manages personal and performance-related data, and also gives you the option to store key payroll info like salary and bank details. This makes Breathe a great back-up for payroll information, especially if you ever switch payroll providers.  

Top tip: Both Breathe HR and Xero are designed to support full GDPR compliance when used correctly.  

 

Final verdict: A smarter way to manage your business  

Choosing separate HR and payroll systems, like Breathe HR and Xero, isn’t a compromise. It’s a strategy. A move toward a more resilient, efficient, and scalable way of working.  

It’s how growing UK businesses ensure compliance, reduce risk, and free up time to focus on what matters most: their people.  

 

 

FAQs

Isn’t it simpler to have one system for HR and payroll?  

Not really. With smart integrations like Breathe HR + Xero, you enjoy the simplicity of a unified experience without compromising performance or flexibility.  

Will it take long to set up the integration?  

Not at all. Breathe’s Xero Payroll integration is quick and intuitive. Most businesses are up and running in a couple of hours.  

What if our payroll needs change as we grow?  

That’s one of the best parts about using separate systems. Your Breathe HR system remains constant, while you can swap or scale your payroll solution without starting over. 

How much does it cost to switch on the integration between Breathe HR and Xero?

No cost, the integration is free.   

Elise

Author: Elise Featley

Elise is Breathe’s Product Marketing Manager, bringing 10 years of marketing know-how and a sharp eye for strategy to the team. With a background in driving product marketing success, Elise has a knack for turning complex features into clear, compelling stories that connect. She’s led go-to-market launches, shaped standout value propositions, and helped scale-ups bring new products to life — always with the customer front and centre. Outside of work, she’s a proud bookworm, happiest on a long walk, and firmly believes there’s nothing in the world a good cup of tea can’t fix.

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