How to Integrate Payroll with Existing HRIS and Accounting Tools

Payroll, HRIS, and accounting often operate in siloes, and that separation creates real challenges. Your teams waste time on manual data entry, the risk of errors and non-compliance grows, and you can’t trust your reporting.

You may know these individual systems well, but feel unsure what effective consolidation looks like in practice. Perhaps you’re cautious about replacing all your tools at once and creating widespread disruption.

That’s why our guide focuses on how to integrate payroll with the tools you already use. Drawing on Deel’s experience managing global payroll integrations, we explore the advantages and practical steps for unifying your system.

The benefits of payroll integration with HRIS and accounting

Connecting payroll systems with HRIS and accounting eliminates inefficiencies and reduces your error rate. It prevents a snowball effect where small mistakes and wasted time accumulate, creating larger issues that affect your bottom line.

Basically, when systems remain disconnected, teams must re-enter the same data across platforms. This reduces productivity and increases the chance of human error. The best-case scenario is that your team wastes more time catching and fixing the mistakes before they cause problems. And the worst-case scenario is that errors slip through the gaps, leading to significant compliance penalties.

For example, HR might classify a worker as a contractor while payroll treats them like an employee. Misclassification like this can incur fines of $25,000 per violation in some US states.

While an integrated payroll system isn’t a silver bullet, it prevents the root cause of many of these challenges. It syncs data in real-time, so your system is always accurate and up to date. And it improves collaboration between departments to help you catch issues more easily when they do arise.

3 methods of payroll integration

There are three ways to connect global payroll with the rest of your system. Each method has tradeoffs in terms of cost, complexity, and scalability, but the right one for you depends on your specific needs.

API integrations

An API is a direct connection between your payroll, HRIS, and accounting. Think of it as a pipeline that enables the different systems to share information and keep each other updated.

Although an API provides a lot of flexibility, it requires expertise to set up and maintain. Its complexity is well-suited for enterprise-level payroll teams with a dedicated IT team for support, but may overwhelm smaller businesses.

Third-party connectors

No doubt you’ve heard of apps like Zapier and Workato. These third-party connectors handle integrations between your payroll, HRIS, and accounting to unify your system.

As you might expect, third-party connectors are less complex than an API. They work well for companies needing a quick, out-of-the-box solution to integrate popular apps. The tradeoff is that they come with added subscription costs for the app, and they’re less customizable than some alternatives.

Unified platform

One way to ensure a high level of integration throughout your system is to invest in a single, unified solution. Platforms like Deel combine HRIS, payroll, and accounting features so your team handles every process in one place.

Consolidating your tools into one system reduces complexity and makes it easier to scale. As teams share one platform, all you have to do is keep adding users and features as your business grows. You don’t have to worry about investing in more software as you enter new markets.

The drawback is that you must replace your HRIS and overhaul your system. But leading providers like Deel guide you through the setup and help you minimize the potential disruption to your operations.

How to prepare for a seamless integration

Preparation can help avoid delays, errors, and costly rework once integration begins. Here are some steps you can take to ensure the transition is smooth.

Audit current systems

Get a clear picture of how payroll, HR, and accounting systems work before connecting them. In particular, map where data currently lives and how it moves between systems.

Take employee data, for example. Do you take a self-service approach where team members can update their records directly? Or do they pass on this information to your HR department to be entered into the system?

Consider all your disconnected system’s current strengths and weaknesses. You can identify duplicate processes, manual handoffs, and long approval chains. Findings from this audit can tell you where a payroll integration could improve efficiency and help solve ongoing issues.

Start with clean data

Fix inaccurate or inconsistent files so they don’t get carried over into the new system. This ensures you experience the least disruption and get the best possible result from your new setup. Here’s what you need to do before you integrate payroll:

• Standardize formatting (names, dates, and codes)
• Verify current information
• Cross-check data across existing systems
• Remove duplicate entries
• Archive inactive employee records

Define integration needs

Decide what you want the payroll software to accomplish. This helps you tailor your setup to your specific business goals and avoid wasted effort.

Start by deciding which data you want to sync across your platforms. For many businesses, this includes a wide range of files, including often overlooked details like contact information, expense reimbursements, and attendance records. Getting as comprehensive as possible ensures you won’t miss opportunities to integrate data and reduce your team’s administrative burden.

Next, decide how often you want to sync data across platforms. Real-time updates might be critical for salary changes and tax information, whereas time-off balances could be handled on a daily or even a weekly basis.

Align with key stakeholders

Get HR, finance, and IT on the same page from an early point in the transition. Each department will have a major role in different parts of the integration process and should understand their roles and responsibilities for everything to run smoothly.

Bring together leaders and representatives from every team well before you start considering vendors. You can agree on a timeline for the transition and the milestones you expect to reach by different points.

Set success metrics

Finally, decide what you want the payroll integration to achieve at different intervals. This helps everyone check that the transition is running smoothly during setup and that you’re getting the expected results. Here are some metrics you might track:

• Productivity levels
• Error rate
• Payroll processing time
• Employee benefits enrollment
• Compliance incidents
• Team satisfaction
• Adoption rates

Don’t forget to measure your current metrics ahead of the integration. You need a clear benchmark to see how much value you’re getting from your new setup and demonstrate its ROI to leadership.

Best practices for a successful integration

Even with the right integration method, success depends on how you manage the rollout and maintain the system. Following payroll best practices can reduce risks, accelerate adoption, and ensure the system continues to deliver value.

Document processes

Documenting every payroll process makes onboarding and managing employees easier. You can share step-by-step instructions for every workflow in a centralized drive on your system. In case anyone has follow-up questions, you can develop a comprehensive FAQ document.

A detailed record also helps you track your progress against old, less efficient processes. In leadership meetings, you can use this documentation to make links between your payroll integration and improved outcomes, making a stronger case for continued investment.

Read our guide on why and how to document your payroll processes for a more detailed look at what to do.

Prepare staff for changes

Effective change management is essential to ensure staff understand and welcome the new processes. 39% of workers say they’re less likely to embrace changes if they don’t understand why they’re happening. Plus, if anybody’s feeling confused about what to do, they’ll be more inclined to use workarounds that allow errors to creep back in.

Besides the documentation mentioned above, announce the new integration in a company-wide message. Explain what changes to expect and when. This ensures everybody understands what they’re supposed to be doing at each stage in the transition, so they’re never blindsided.

Then provide employee onboarding sessions for each department based on their typical responsibilities. For example, IT should understand the protocol for adding new users to the system, and finance should know how to generate reports for bookkeeping.

Prioritize data security

Poorly handled integrations can leave sensitive information vulnerable, so securing it must be a top priority. This starts with finding a vendor that meets high industry standards for data protection and has certifications like SOC 2 and ISO 27001.

Within your organization, ensure that staff only have access to the minimum data required to perform their duties. This reduces the risk of someone making a mistake and unwittingly exposing data. IBM research has found that most breaches come from within businesses, so limiting access to sensitive information could significantly decrease risk.

Verify compliance support

Confirm your payroll integration supports compliance in all the areas where you operate and beyond. If it leaves gaps in your coverage, you’ll have to add extra tools, making your system more scattered.

The first step is to ensure the vendor applies updates as soon as regulations change. Payroll laws are constantly evolving, and even a small delay leaves you at risk of a penalty. It’s a bonus if you can find a provider like Deel with a continuous compliance hub that sends you updates in advance and explains what they mean in plain language.

The next step is to check that the payroll integration supports local filing formats, contribution rules, and recordkeeping requirements. These vary considerably across regions, so a one-size-fits-all approach will lead to compliance issues.

Test integrations thoroughly

Testing your integration before rollout helps you catch issues before they disrupt operations. Run trial payrolls and data syncs to confirm everything is running smoothly. You can check the accuracy and the timing to ensure you won’t experience any issues.

Consider having your team test the payroll process as well. You want to be confident they can handle the system before they assume full responsibility for different tasks.

Conduct regular reviews of integrations

As your business needs evolve, continuously monitoring and adjusting the system ensures it’s always helping you achieve your goals. Schedule annual or biannual reviews to check your payroll integration.

Reviews can follow many of the same steps as above. You can audit your data, test processes, and compare metrics over time. As you notice areas for improvement, you can update workflows and re-train your team.

Additionally, collecting feedback from your team can give you a more comprehensive idea of what’s working and what’s not. Arrange meetings with representatives from HR, finance, and IT to get their input. Meanwhile, send quick, anonymous surveys to understand the day-to-day employee experience of using the system.

Choosing the right integration partner

Success depends on the vendor you choose. The right integration partner can help you through setup and ensure you make the most of all the features. Here are some key factors to consider as you choose a global payroll provider:

• Compatibility with existing tools: The partner should connect smoothly with your current tools so you don’t have to replace anything you already rely on. Look at their integration marketplace on their website to check that they cover the essentials
• Global compliance expertise: Payroll is subject to complex tax and labor laws, especially if you operate internationally. A provider with an outstanding track record in compliance can help you set up your system to minimize the risks
• Accessible customer support: When issues arise, your team needs someone with expertise to turn to. Prioritize an integration partner with 24/7 support across a variety of channels so you’re not kept waiting while problems escalate
• Transparent pricing: Predictable fees and clear pricing make it easier for you to budget so you can manage your integration without any financial strain
• Scalability: Your integration may look very different in a year as your business needs change. Providers should be able to handle more employees, geographies, and systems without forcing you to start from scratch
• Security standards: HR and payroll data are sensitive, so providers must have high-quality encryption. They must also support security with features like role-based access, two-factor authentication, and unique passcodes
• Implementation support: Integrations can be complex even if you have the right technical expertise. Choose a provider that can provide onboarding, training, and guidance to make the process smoother

Unify payroll, HRIS, and accounting with Deel Payroll

Integrating payroll isn’t just about cutting down manual work. It also gives you more reliable data across systems, stronger collaboration between departments, and more comprehensive insights. As employees see you’ve got a system that truly works, you can also inspire greater confidence and trust in your employer brand.

Deel Payroll can make this possible by connecting with the HR and accounting platforms you already use. Our platform offers:

• Prebuilt integrations with leading solutions
• A unified dashboard to bring all your data together
• Automated payroll runs with real-time syncs
• Compliance support across 130+ countries
• Enterprise-grade security
• Customizable reporting and analytics
• Scalable infrastructure that grows with your business

Looking to integrate payroll? Book a demo with the Deel team to explore our platform and see how we can unify your operations across regions and departments.