Best payroll software for accountants: choosing the right solution

Digital finance tools are now a key part of running a business. According to the UK Government's Longitudinal Small Business Survey 2024, 80% of SMEs using business software use accountancy software, while 57% use payroll software to support their operations. As a result, many businesses are looking for accounting and payroll software that can automate routine processes and integrate payroll with wider financial management.

Below, we'll explore what to look for when looking for the best payroll software for accountants, including the differences between some of the main providers, as well as how to find the right solution for your business or accounting practice.

What should accountants look for in payroll software?

Finding the right payroll software for accountants depends on the needs of your practice or business. While every organisation has different requirements, the best solution should simplify payroll processing, reduce manual administration and help ensure compliance with UK payroll legislation.

For accountants managing payroll across multiple clients, software should also make it easier to handle recurring tasks, maintain accurate records and access payroll information quickly.

Key features for accountants

When comparing payroll software for accounting firms, it's worth looking beyond basic payroll processing and considering features that support long-term efficiency and scalability.

Some key features to look for include:

• Automatic payroll calculations to reduce manual work and improve accuracy.

• HMRC submissions, including Real Time Information (RTI) reporting.

• Workplace pension management to support automatic enrolment duties.

• Employee self-service portals allow employees to access payslips and update personal information.

• Payroll reporting and analytics to provide greater visibility over payroll costs and trends.

• Integrations with accounting software and other business systems to minimise duplicate data entry.

As your client base or workforce grows, choosing software that can scale alongside your business can help minimise disruption and reduce the need to switch systems later.

👉 To note 

If you're managing payroll for multiple clients, consider whether the software supports multi-company payroll, user permissions and centralised reporting. These features can make day-to-day payroll management significantly more efficient.

Features that save time

One of the biggest advantages of using online accounting and payroll software is automation. Repetitive payroll tasks that were once completed manually can now be streamlined, allowing accountants and payroll professionals to spend more time supporting clients and less time on administration.

Time-saving features may include:

• Automatic payroll calculations and statutory payment updates.

• Scheduled payroll runs.

• Digital payslip distribution.

• Leave and absence management.

• Employee self-service for updating personal details.

• Automated reminders for payroll deadlines and compliance tasks.

• Integration with time tracking and attendance systems.

Choosing software that automates routine processes can also help reduce the risk of manual errors while creating a more consistent payroll process across your organisation or client portfolio.

⚠️ Warning: Relying on manual payroll processes or disconnected systems can increase the risk of duplicate data entry, payroll errors and additional administrative work. As payroll requirements become more complex, integrated software can help improve accuracy and maintain consistency.

Can accounting software include payroll?

Although payroll and accounting software are closely related, they are designed to support different business functions. 

Accounting software with built-in payroll

Accounting software helps businesses manage their day-to-day finances by recording income and expenses, generating financial reports and supporting bookkeeping tasks. Depending on the platform, it may also include features such as invoicing, bank reconciliation, cash flow reporting and tax management.

Some businesses use accounting software used for payroll, or choose bookkeeping and payroll software that combines both functions in one platform. However, payroll features can vary significantly between providers, so it's important to understand exactly what's included before making a decision.

Separate payroll software

Even if an accounting platform includes payroll capabilities, many organisations choose dedicated payroll software to manage employee pay more efficiently. Payroll involves more than calculating wages, it also includes processing statutory payments, managing workplace pensions, submitting information to HMRC and maintaining accurate employee payroll records.

A dedicated payroll solution can also automate routine tasks, reduce manual administration and provide features such as employee self-service, leave management and payroll reporting. For businesses looking for an accounting payroll system, choosing software that integrates payroll with accounting can help streamline financial processes while ensuring each function has the tools it needs.

📌 Example: A small business may use accounting software to manage invoices, expenses and financial reporting, while using dedicated payroll software to calculate employee pay, submit payroll information to HMRC and manage workplace pensions. Integrating the two systems helps keep financial and payroll data aligned.

What accounting and payroll software is available in the UK?

How do payroll software providers differ?

While all payroll software is designed to help businesses pay employees accurately and remain compliant with payroll legislation, providers can differ significantly in the features they offer and the organisations they are designed to support. Some solutions focus primarily on payroll processing, while others combine payroll with HR tools, employee self-service and integrations with accounting software. There are also platforms tailored to accountants managing multiple clients, as well as solutions for small businesses, growing SMEs or larger organisations with more complex payroll requirements.

Comparing accounting and payroll software

The right solution will depend on your business size, payroll complexity and existing technology. Comparing the different types of accounting and payroll software available can help you identify a platform that best supports your current needs while remaining scalable as your business grows.

How much does accounting and payroll software cost?

The cost of accounting and payroll software can vary depending on the size of your business, the number of employees you manage and the features you need. Some providers charge a fixed monthly subscription, while others use a pricing model based on the number of employees or payroll processed. Additional costs may also apply for optional features such as HR management, time tracking, reporting or premium customer support. The total cost of ownership may also depend on implementation, training and any integrations with your existing accounting software.

👉 To note: Some payroll providers offer free trials or personalised demonstrations, allowing you to explore the software before committing to a subscription. Comparing what's included in each pricing plan can help you identify the best value for your business rather than simply choosing the lowest-cost option.

How to choose the best payroll and accounting software for your business

Choosing the right business accounting and payroll software starts with understanding your organisation's current needs and future plans. While some businesses require a simple solution to process payroll, others may benefit from software that combines payroll with HR features, reporting and integrations. 

💡 Good to know: If you currently use separate accounting and payroll systems, look for software that integrates with your existing tools. This can help reduce duplicate data entry and improve the flow of information across your business.

Questions to ask before choosing software

Before investing in a payroll solution, it's worth considering how well it fits your business and payroll processes. Asking the right questions can help you identify software that meets your current requirements while supporting future growth.

Some questions to consider include:

• How many employees do you process payroll for?

• Will multiple users or teams need access to the software?

• Does the software integrate with your existing accounting platform?

• Can it automate payroll calculations and statutory reporting?

• Does it support employee self-service and digital payslips?

• Will it continue to meet your needs as your business grows?

If you're looking for small business payroll and accounting software, ease of use, automation, and ongoing support may be just as important as the number of features available.

👉 To note: Choosing software based solely on price may not deliver the best long-term value. Consider how much time automation, integrations and built-in compliance features could save your business.

Features that matter most

The right payroll software should do more than process employee pay. It should help simplify payroll administration and integrate with the wider systems your business relies on.

When comparing accounting software with payroll for small businesses, consider whether the solution offers:

• Automated payroll calculations and HMRC submissions.

• Integration with accounting software and other business tools.

• Employee self-service for accessing payslips and updating personal information.

• Leave and absence management.

• Payroll reporting and analytics.

• Secure document storage.

• Regular software updates to support changes in payroll legislation.

• Reliable customer support and training resources.

📌 Example: A business with 75 employees may initially only need payroll processing, but as it grows, it may also require leave management, employee self-service and reporting. Opting for software that offers these features from the outset can make it easier to scale without changing systems later.

Managing payroll doesn't have to be time-consuming. With the right accounting and payroll software, accountants can automate routine tasks, reduce manual errors and spend less time on administration. Book a free demo to see how an integrated payroll solution can support your accounting business now and in the future.

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