The Best In-House Payroll Software In 2025

What Is In-House Payroll Software?

In-house payroll software is a system that companies use to manage their own employee pay. Instead of hiring an outside company, they handle payroll tasks internally. This software calculates salaries, manages deductions, handles taxes, and ensures that employees get paid correctly and on time. It keeps all important information, like working hours, benefits, and leave, organized, so HR or finance teams don't have to do it manually. This saves time and reduces errors, which is beneficial for both employers and employees.

In-house payroll software is a reliable, efficient, and customizable way for companies to manage payroll. It gives businesses more control over their processes, keeps data secure, and helps teams work more efficiently and accurately. Whether a company is small or established, having dedicated payroll software can significantly enhance accuracy, productivity, and employee trust.

Table Of Contents

• Benefits Of In-House Payroll Software
• Cons Of In-House Payroll Software
• Who Is Responsible For In-House Payroll? Accounting Vs. HR
• What To Pay Attention To When Selecting An In-House Payroll System
• Overview Of The Best In-House Payroll Software In 2025
  • Staffology Payroll (By IRIS)
  • BrightPay
  • Sage Business Cloud Payroll
  • Gusto
  • OnPay
  • Paychex Flex
  • Rippling
  • PayFit
  • Papaya Global
  • Remote
• Conclusion

Benefits Of In-House Payroll Software

Managing payroll is one of the most critical tasks for any business, and using in-house payroll software can make the process smoother, faster, and more secure. Here are some of the main benefits:

• Full control over payroll data
  Your company has complete control over its payroll data. You decide who accesses it, how it's stored, and when it's processed.
• Enhanced data security
  In-house software keeps data on your own servers, reducing the risk of breaches from third-party providers.
• Customization according to company needs
  The software can be tailored to your policies, benefits, leave structures, and tax rules.
• Real-time access to payroll information
  You can access payroll information whenever you need it. Whether it's checking employee salary history, generating payslips, or reviewing tax deductions, it's all just a few clicks away.
• Faster problem-solving and updates
  Since your payroll team handles the software directly, any glitches, errors, or updates can be resolved quickly.
• Cost savings
  While the initial setup may seem expensive, in-house payroll software can save money over time by reducing subscription fees paid to external payroll providers.
• Integration with existing systems
  In-house payroll software can be integrated seamlessly with your HR, accounting, and attendance systems.
• Compliance with local regulations
  With in-house software, your company can adapt the system quickly to stay compliant with the latest legal changes.
• Detailed reporting and analytics
  The software allows you to generate detailed reports, like salary distribution, tax deductions, overtime, and bonus calculations.
• Employee self-service options
  Many in-house payroll systems include portals where employees can view payslips, submit leave requests, and update personal information.
• Improved accuracy and reduced errors
  Automation through in-house software ensures accurate calculations of salaries, taxes, and benefits.
• Scalability for growth
  As your business grows, in-house software can handle a larger workforce.

Cons Of In-House Payroll Software

While in-house payroll software offers many benefits, it's not without challenges. Here are some of the cons:

• High initial setup cost
  Implementing an in-house system can be expensive, requiring software licenses, hardware, and IT support.
• Maintenance responsibility
  Unlike cloud-based payroll services, maintaining in-house software is your team's responsibility. This includes regular updates, bug fixes, and server management.
• Requires skilled staff
  Running payroll in-house demands trained personnel who understand both payroll processes and the software.
• Risk of technical issues
  If the system encounters technical problems, payroll processing could be delayed. Without a dedicated IT team, this can be challenging.
• Responsibility for compliance
  Keeping the software up to date with tax laws and regulations falls entirely on your company.
• Risk of data loss
  You are responsible for backing up payroll data and ensuring you have a plan in case it gets lost or destroyed.
• Time-consuming implementation
  Setting up an in-house payroll system can take weeks or even months.
• Potential for human error
  While the software reduces calculation mistakes, errors can still occur.
• Less flexibility for smaller companies
  Smaller organizations may not fully use all features, which makes it expensive.

Who Is Responsible For In-House Payroll? Accounting Vs. HR

When it comes to managing payroll, one of the most common questions in a company is who is responsible for it: accounting or HR? The answer isn't simple since payroll involves both departments. However, the key is to understand their roles.

HR manages the company's staff. It handles hiring, onboarding, employee records, benefits, and time tracking, all of which impact payroll. For instance, HR tracks vacation days, sick leave, overtime, bonuses, and salary changes. If HR does not keep this information updated, payroll can be wrong. On the other hand, accounting focuses on money. It makes sure the company's financial records are accurate, calculates taxes correctly, and ensures timely payments. For payroll, accounting typically deals with calculations, deducting taxes, preparing paychecks, and ensuring compliance with labor laws and tax regulations. They also manage financial reporting and record payroll expenses properly.

So, to answer who is responsible for payroll in-house, know that HR and accounting share the responsibility, but their roles are different. HR provides accurate employee information, while accounting handles the financial side. The best payroll processes happen when both departments communicate well, work closely together, and respect each other's expertise.

What To Pay Attention To When Selecting An In-House Payroll System

Team Evaluation

First, think about your team. How comfortable are they with technology? Do they need something simple, or can they handle advanced features? A system that is too complicated can cause more issues than it solves, while one that is too basic may not keep up with your company's growth. Ensure the software fits your team's skill level.

Payroll Tax Management And Reporting

Payroll involves taxes, and mistakes can be costly. Look for a system that simplifies tax calculations and ensures compliance with local and national regulations.

Security

Payroll data is sensitive. A good system should have robust security measures, including encryption, secure access controls, and regular backups. You want to protect your employees' information and your company from potential breaches.

Payment Flexibility

Employees have different ways they like to get paid. Can the system offer direct deposits, paper checks, or mobile payments? Allowing different payment methods makes things easier for both your team and staff.

Employee Self-Service

Modern payroll systems often include self-service portals where employees can access pay stubs, tax documents, and benefits information. This feature reduces admin work for your HR team and empowers employees to manage their own information.

Integration Capabilities

Your payroll system should integrate smoothly with your HR, accounting, and time-tracking software. Integration reduces manual work, minimizes errors, and provides a complete picture of your business finances.

Vendor Reliability

Choose a reliable vendor. Look at their reviews, ask for references, and check how long they have been in business. Good vendors offer consistent support, updates, and improvements, which are essential for long-term success.

Hardware

Some systems need specific hardware. Check if your current setup can run the software without expensive upgrades. If you need new hardware, think about whether the cost fits your budget and future plans.

Data Transfer And Conversion

Check whether the software can easily import your existing employee data, historical payroll records, and tax information. Smooth data transfer saves time and reduces the risk of errors.

Implementation Resources

Finally, consider the support you'll get during implementation. Does the vendor provide training, guides, or on-site assistance? Good implementation resources help your team get up to speed quickly and ensure the system runs smoothly from day one.

Overview Of The Best In-House Payroll Software In 2025

1. Staffology Payroll (By IRIS)

Suitable For

It's suitable for small- to mid-sized UK-based businesses, especially those that want a cloud-based payroll solution.

Features

• Cloud access works on desktop or mobile.
• Integrations with popular accounting and bookkeeping tools (e.g., Xero, QuickBooks) and HR platforms.
• Payroll processing, including pay‑run calculations, automated tax/pension submissions (for UK businesses), and payslip generation.
• Option to expand into a broader HR suite (depending on business needs).

Pricing

• £39/month for up to 19 payslips per month.
• For 20–50 payslips, the cost is £39 + £1.95 per payslip beyond the initial 19.
• For over 50 payslips, the pricing is typically custom.

Pros

• Transparent, usage-based pricing.
• Cloud-based so that you can access payroll from anywhere.
• Integrations reduce the need for manual payroll synchronization with accounting or HR platforms.
• Scales well as you grow.

Cons

• For very small businesses, the per-payroll slip cost may feel high compared to simpler/payroll‑only tools.
• Might not offer the advanced HR or benefits features that a larger company needs.
• Less ideal if you have highly complex payroll needs.

2. BrightPay

Suitable For

This payroll solution is ideal for small businesses, freelancers, and micro-businesses that want an easy and reliable way to manage payroll.

Features

• Full support for payroll compliance.
• The hybrid model combines desktop processing with cloud-based backup and employee self-service options, as needed.
• Transparent pricing, rather than per-employee/month fees.

Pricing

• Approximately £149 per year for up to three employees (for a small-sized license).
• Pricing scales with the number of employees and the functionality required.

Pros

• Very affordable for small businesses.
• Reliable and compliant for standard payroll tasks.
• Great for businesses that prefer a predictable, fixed-cost model.
• Flexibility.

Cons

• May lack advanced HR, benefits, or global payroll features.
• Less ideal for larger companies or companies with complex payroll structures.
• Using desktop processing might not be the best choice for teams that want complete flexibility in the cloud from the beginning.

3. Sage Business Cloud Payroll

Suitable For

Small to medium-sized businesses that want a scalable payroll solution, especially if they already use or plan to use other tools from the same ecosystem.

Features

• Simple, guided payroll workflows.
• Automatic updates to stay compliant with tax and payroll legislation.
• Reporting tools to monitor payroll cost, employee payroll history, etc.

Pricing

• The entry-level plan costs approximately £7 per month for up to 5 employees, though this may vary depending on the country.
• Pricing increases as the number of employees grows.

Pros

• Cost‑effective for small teams starting out.
• Scalable as your company grows.
• Reliable vendor with a reputation in accounting and payroll.
• Integrates well with broader accounting or financial workflows if used in the full Sage ecosystem.

Cons

• Larger teams or more complex payroll needs may lack advanced HR or benefits features.
• Less customization compared to large-scale platforms.
• Some features may seem basic compared to those of full-featured systems.

4. Gusto

Suitable For

Small- to medium-sized businesses, especially those seeking a modern, user-friendly payroll, HR, and benefits solution with minimal hassle.

Features

• Full payroll (tax calculations, automatic filings, direct deposit), multi-rate pay, unlimited payroll runs.
• Built-in HR tools, including onboarding, benefits administration, time tracking (depending on plan), PTO and leave management, and employee self-service.
• Integration with many third‑party apps.

Pricing

• Simple: $49/month plus $6 per employee per month.
• Plus: $80/month plus $12 per employee per month.
• In higher-tier plans (Premium) with more features and support, the cost increases accordingly.

Pros

• Very user-friendly and intuitive interface.
• An all-in-one platform with payroll, HR, and benefits handling.
• Automated tax compliance and filings.
• Employee self-service and modern UI help both admins and staff.

Cons

• As the team grows (or needs more advanced HR features), costs can scale up significantly.
• For businesses outside supported regions (e.g., outside the US), Gusto may be less useful.
• Some advanced features (especially HR/time tracking) are available only in higher-tier plans.
• It may be overkill if you only need simple payroll and no additional HR services.

5. OnPay

Suitable For

Small businesses, nonprofits, or organizations seeking a simple but reliable payroll system, without paying a lot for features they won't use.

Features

• Payroll processing and automated tax filing for W-2s and 1099s.
• Supports unlimited payroll runs, multiple pay rates, and contractor support (where needed).
• Onboarding tools, PTO/sick leave tracking, and HR document storage.
• Simple, flat-fee pricing.

Pricing

• $40/month plus $6 per employee per month.
• A one-month free trial is often offered.

Pros

• Transparent, predictable pricing.
• Covers all essential payroll needs such as tax filing, pay runs, onboarding, PTO, and contractor support.
• Good value for small companies that don't need complex HR or enterprise-level features.
• Easy to set up and use, ideal for small teams or those new to payroll.

Cons

• It may be too basic for larger companies or those requiring global payroll or advanced HR solutions.
• Fewer integrations than some other platforms.
• Limited advanced customization.

6. Paychex Flex

Suitable For

Small to mid-sized companies that want not just payroll but also HR support, benefits, retirement plan handling, and other extended services.

Features

• Payroll processing with W-2/1099 support, automated tax filing, direct deposit, or checks.
• Employee self-service portal, online onboarding, new‑hire reporting, and background checks (depending on plan).
• Optional HR and benefits modules, like retirement plan management, compliance tools (OSHA, workers' comp), HR documentation, and reporting.
• Mobile accessibility to run payroll, access pay stubs, and check reports on the go.

Pricing

• Essentials tier: $39/month plus $5 per employee per month.
• Additional features, modules, or advanced HR and benefits tools typically require higher-tier plans with custom pricing.

Pros

• Scalable solution.
• Combines payroll, HR, benefits, and compliance.
• Reliable and established.
• Useful for businesses that want to offer retirement plans or benefits, in addition to salaries.

Cons

• Add-ons and extra modules can quickly increase total cost.
• Interface and workflows sometimes feel dated compared to newer, more modern platforms.
• For very small teams, using simpler tools may be a better choice than investing in more complex options.
• Some features may need integrations or separate modules.

7. Rippling

Suitable For

Fast‑growing companies, global teams, or companies that want to manage HR, IT, payroll, compliance, and finance in a unified system. Great if you expect to grow or scale internationally.

Features

• Payroll, HR, IT, and finance in one modular platform, allowing employee management, pay, benefits, and even app management from a single dashboard.
• Global payroll support, which handles employees in more than 160 countries, makes it useful for international or remote-first teams.
• Workflow automation.
• Employee self-service portal, benefits administration, expense and spending management, and reporting.

Pricing

• Base platform: $8 per user per month (for core HRIS).
• The Payroll module adds extra features and is listed at about $35 per user/month, but the total cost becomes custom depending on the modules and features needed.

Pros

• Extremely powerful and flexible.
• Great for global, remote, and multi-country teams or businesses planning to expand internationally.
• You pay only for what you need and can add HR, IT, and finance modules as required.
• Automation reduces manual workload, reduces human errors, and improves compliance and auditability.

Cons

• Pricing is less transparent, as you often need to request a custom quote.
• For small businesses or startups, it might be excessive.
• Some users find customer support slower or less direct.
• Setting up complex workflows or integrating multiple modules can take time and expertise.

8. PayFit

Suitable For

Small to medium-sized businesses (especially in Europe) that want a cloud-based payroll and basic HR solution, with straightforward pricing and relatively easy onboarding.

Features

• Automated payroll calculations, payslip generation and distribution, and support for statutory tax and social‑contribution submissions.
• Employee portal, leave and absence management, onboarding and offboarding, document generation and electronic signatures, and basic HR workflows.
• Integration capabilities with accounting software or existing HR tools (via OpenAPI), making it easier to sync payroll data with your accounting or ERP systems.

Pricing

• Plan "Light": Around £5 per employee per month, plus a £29 monthly subscription fee.
• Plan "Standard": Around £6 per employee per month, plus a £59 subscription.
• Plan "Premium": Approximately £7 per employee per month, plus £119 subscription.

Pros

• Very user-friendly.
• Payroll and basic HR on the same platform.
• No long‑term lock‑in. Transparent, predictable pricing.
• Automates repetitive tasks, reduces manual errors, and integrates well with accounting workflows.

Cons

• Report generation and analytical features are somewhat limited.
• For complex payroll structures or very large teams, the tool might feel too basic.
• Some users report occasional performance issues.

9. Papaya Global

Suitable For

Companies with an international or multi‑country workforce that need global payroll processing, compliance across jurisdictions, and scalable payroll and HR infrastructure.

Features

• Global payroll automation with built-in compliance for many countries.
• Unified dashboard for payroll, payments, compliance, and workforce analytics.
• Option for more advanced global HR services, including contractor management, Employer-of-Record (EOR) services, benefits and compliance management, and analytics.

Pricing

• The Full-Service Payroll plan starts at around $12 per employee per month.
• More comprehensive packages (with EOR, contractor management, benefits, and global compliance) are priced higher; cost depends on services, employee count, and countries covered.

Pros

• Great for businesses with distributed teams across countries.
• Consolidates many HR, payroll, and administrative needs into one platform.
• Payroll, payment infrastructure, global compliance, and analytics are essential for scaling companies.

Cons

• More expensive than simpler, small‑business‑oriented tools.
• It may feel unnecessarily complex for small teams or purely local businesses.
• Integration with third-party software may be more limited compared to some local payroll and HR tools.

10. Remote

Suitable For

Companies with an international workforce or a remote-first model that hire employees or contractors across multiple countries and need global payroll, compliance, and ease of cross-border payments.

Features

• Global payroll processing and compliance for employees and contractors in many countries.
• Employer‑of‑Record (EOR) services are available in many jurisdictions.
• Employee self-service, time-off and contractor management, the ability to pay in different currencies, and the ability to manage cross-border payments securely and on time.

Pricing

• Payroll services start at approximately $50 per employee per month.
• Employer‑of‑Record and contractor‑management plans have higher costs. The price often requires a custom quote depending on workforce distribution.

Pros

• Excellent choice for remote or global teams.
• Reduces admin burden as all payroll, compliance, and payment operations are managed centrally.
• Good for companies expanding internationally or hiring freelancers and contractors globally.

Cons

• For small teams or local businesses, the cost may not be worth the complexity.
• Using a system may provide more features than needed for companies with few employees or simple payroll, which can create unnecessary work.
• Relying on outside providers for compliance and specific country setups can reduce the level of internal control compared to handling payroll entirely in-house.

Conclusion

Choosing the right in-house payroll software is all about finding the perfect balance between simplicity, scalability, and compliance. Whether you run a small local business or manage a growing global team, the ideal solution should streamline payroll, reduce errors, and integrate seamlessly with your HR and accounting systems. So, keep searching; there's a tool for every business size and need.