The 12 best enterprise payroll software for large businesses in 2025

Large organizations face numerous challenges when it comes to payroll processing. Between managing hundreds—or even thousands—of employees, keeping up with ever-changing labor laws, and maintaining ironclad data security, HR teams have their hands full. That’s why choosing the right enterprise payroll system is so crucial. This guide is aimed at those looking to streamline payroll processing through features like multi-jurisdictional compliance, customizable pay structures, employee self service, automation, and integrations. By optimizing your payroll system, you can save your HR staff significant time and energy, reduce errors, and address your business needs more efficiently.

In this article, we’ll highlight HR software for large companies that can also handle payroll tax filing, benefits administration, time tracking, and much more. We’ll dig into each option’s features, discuss pros and cons, and help you find the top payroll software for your organization.

Whether you’re looking for advanced payroll services, robust compliance tools, or automatic payroll capabilities, one of these payroll solutions should fit the bill.

What is enterprise payroll software?

Enterprise payroll software is a payroll solution designed to handle the complexities of payroll management for large businesses.

 Unlike small businesses, enterprises generally have extensive HR operations, including onboarding, benefits administration, tax calculations, time tracking, direct deposit management, and more. A good enterprise payroll system centralizes and automates these tasks, making it easier for payroll administrators and HR staff to manage payroll for a multi-state or even global workforce.

Below are some important features that payroll software for large companies should include:

• Multi-jurisdictional compliance: Enterprise payroll software stays up to date with local, state, and federal regulations to make sure taxes are filed correctly and compliance is maintained across different regions.
• Customizable pay structures: Enterprises often have diverse roles and compensation packages, including variable pay, bonuses, deductions, and garnishments. Good payroll software can adapt to these structures seamlessly.
• Employee self-service portals: A portal for employee self service lets your workforce access pay stubs, update personal data, and see deductions or benefits information without requiring constant HR assistance.
• Automation features: Automatic payroll runs, automated tax calculations, and built-in time tracking reduce manual work for payroll administrators and support timely payroll processing.
• Integration capabilities: Integrations with accounting software, time and attendance systems, and other HR software can further streamline payroll processes and reduce data errors.

12 best payroll software for large businesses

Below are some of the best payroll software tools for enterprises in 2025. Each one offers distinct strengths in payroll processing, plus other features like time tracking, benefits administration, and compliance management. We’ll highlight their key features and pros and cons so you can pick the right payroll solution for your business needs.

1. Rippling

Rippling offers more than just payroll—it’s a fully featured human capital management platform that you can easily configure to meet your needs so you can manage all your people operations at scale. 

What sets Rippling apart from other enterprise payroll solutions is that every app in Rippling—from Payroll to Recruiting, Time and Attendance, Benefits Administration, Performance Management, Device Management, Expense Management, and more—is built on a single source of truth for employee data. That means you can automate any process in Rippling, from routine processes like onboarding to complex ones like global compliance. Manage employees with modules that actually talk to each other. For example, if you offboard someone, Rippling knows to cut their last check and deprovision their app access. Build the platform you need from a library of natively built applications and third-party integrations. Rippling’s unified data model gives you unparalleled configurability in—and across—your tools.

Rippling also empowers HR leaders to deliver more value to their company by reporting on trends and insights that impact the business, thanks to unified data across modules. Quickly uncover insights on productivity, costs, or virtually any topic you can think of, when data is available at your fingertips, even from third-party apps.

Key features for enterprise:

• Unified HR software platform
• Automates any workflow, from onboarding to tax filing, benefits administration, and payroll services
• Robust reporting, including payroll reports
• User-friendly employee portal for employee self service
• Extensive software integrations for accounting software and other tools

Pros:

• Highly scalable for enterprises
• Customizable HCM that HR and payroll administrators can set up how they want

Cons:

• May come with a learning curve for some users

2. Gusto

Many businesses choose Gusto for its easy-to-use interface, and it has long been a payroll provider aimed at small businesses looking for a straightforward platform. 

Its newer features cater to larger HR operations, covering payroll processing, benefits administration, and time tracking, but Gusto is still limited for enterprise organizations—it can’t handle multiple EINs and doesn’t integrate with as many third-party tools as other solutions, which limits its ability to scale. Gusto is also limited in its reporting—it doesn’t offer Excel functionality like pivot tables or formulas, and its data isn’t unified, so you can’t report on data across your HR, IT, Finance, and third-party systems.

Key features for enterprise:

• Automated payroll services with tax filing
• Employee self service for downloading pay stubs and managing deductions
• Built-in time tracking tools

Pros:

• Simple, straightforward, and easy to use
• Good for smaller businesses

Cons:

• Less scalable than some other solutions
• May lack advanced analytics that some enterprises require

3. TriNet

TriNet offers a Professional Employer Organization (PEO). When working with a PEO, a business enters into a co-employment relationship, where they remain responsible for directing and supervising employees and all business decisions, and the PEO helps take payroll, benefits, HR and compliance work off their plate.

A PEO like TriNet can be the right choice for scaling businesses, but can be limiting for enterprise organizations. Trinet is one of the most expensive PEOs in the industry, charging businesses per W-2 per month—plus hidden fees—which means costs balloon as your headcount grows. Plus, if you decide to transition off a PEO like TriNet as your company scales, it’s notoriously difficult to do. You have to rip out the PEO’s systems and start over from scratch implementing new ones—a time-consuming and costly process.

Key features for enterprise:

• PEO that offers comprehensive HR solutions
• Guidance on compliance

Pros:

• Highly automated payroll processes, including payroll tax filing
• HR advisory services

Cons:

• Less scalability
• Less flexibility for growing businesses or organizations that want to move HR in-house

4. ADP

One of the most recognized names in payroll services, ADP offers solutions for both small businesses (ADP Run is its specialized product often used by smaller businesses) and large enterprises. Its enterprise platform provides automatic payroll, benefits administration, time tracking, compliance management, and more.

For enterprise organizations, there are a few key areas where ADP falls short. First, ADP isn’t able to automate as many workflows as some other payroll systems. Since data isn’t unified in ADP, you can’t build custom workflows across any HR module, nor can you trigger actions based on any event you choose.

That also means ADP’s reporting is limited compared to other payroll software solutions. ADP doesn’t offer custom cross-module reporting or Excel-functionality, and you can’t report on data across your HR, IT, Finance, and third-party systems or control access to data based on any employee attribute.

Key features for enterprise:

• Multiple products to meet different business needs
• Robust integrations with third-party tools
• Customizable pay structures and payment options

Pros:

• Long-standing reputation in the payroll provider market
• Broad suite of HR tools beyond payroll processing

Cons:

• Data isn’t unified
• Limited payroll reporting and analytics compared to other platforms
• Some advanced features may require add-on costs

5. Paychex

Paychex is another well-known payroll provider that supports other HR features from payroll management to tax filing to time tracking. Its dedicated Paychex Flex platform aims to make online payroll easier and more convenient. 

But for enterprise organizations, Paychex has drawbacks—many companies quickly outgrow Paychex because it only offers limited HR capabilities and basic functionalities. It also runs on a system built decades ago that hasn’t been updated to suit many modern business needs, like employee self service portals and integrations with third-party software tools.

Key features for enterprise:

• 24/7 support
• HR suite with tools like onboarding, benefits administration, payroll reporting, etc.

Pros:

• Multiple solutions for different business needs
• Customizable, modular platform

Cons:

• Not as scalable as some other platforms
• Interface can feel dated compared to other platforms

6. BambooHR

Though primarily known as an HR software, BambooHR offers payroll services as an add-on to help HR staff manage payroll on top of other HR tasks like time tracking, hiring and onboarding, and reporting. BambooHR is particularly known for its employee self service features.

But while BambooHR typically meets the needs of companies with fewer than 150 employees, customers find it lacks the depth, breadth, and configurability for larger and scaling businesses—it doesn’t offer a full HCM suite with advanced workflows, headcount planning, or learning management features, doesn’t offer advanced permissions, and doesn’t have automatic localization features.

Another potential problem for enterprise organizations is that BambooHR doesn’t track federal, state, and local laws across all 50 states to automatically set compliance policies, which puts customers at risk of infractions.

Key features for enterprise:

• Mobile-friendly employee portal
• Centralized payroll reports and analytics

Pros:

• Clean, intuitive user interface
• Transparent pricing

Cons:

• Less scalable and configurable than some other payroll software
• Doesn’t automatically track compliance like some other payroll systems do

7. Oracle

Oracle’s payroll software module is part of its large suite of enterprise HR software solutions. It focuses on payroll processing, tax calculations, and compliance in multiple locations, making it suitable for global enterprises.

Where Oracle may fall short for large enterprises is how it fits into your tech stack. Today’s businesses work with many technology tools, and Oracle customers note in online reviews that it integrates with fewer third-party tools than other payroll software providers. It’s also less customizable than some other solutions, and for large companies that need a configurable solution, that may make or break their choice.

Finally, customers note that Oracle is complex and time-consuming to implement—something to keep in mind when comparing different solutions and timelines.

Key features for enterprise:

• Comprehensive payroll management with global compliance support
• Analytics and reporting tools
• Integrates with Oracle’s full enterprise resource planning stack

Pros:

• Scalable for large (and global) organizations
• Well-respected brand with proven reliability

Cons:

• Customers complain it’s complex and difficult to implement
• Fewer integrations with third-party tools than some other platforms

8. Justworks

Justworks simplifies HR operations by bundling payroll services into a single platform with other features like benefits administration and compliance. It’s well-suited for small businesses, but what about enterprise organizations?

Justworks offers a PEO, which attracts smaller businesses and growth-minded organizations. But it doesn’t offer advanced HRIS, IT, or Spend capabilities, which limits its ability to scale with its customers. That means it may not be the right fit for enterprise organizations—or businesses with an eye toward rapid growth or expansion.

Justworks also doesn’t offer robust automation or reporting capabilities like some other payroll platforms. It doesn’t have a customer workflow builder, and you can’t create custom reports with any level of data because data isn’t unified within the platform.

Key features for enterprise:

• Streamlined payroll processing with tax filing features
• PEO and other HR features

Pros:

• Easy-to-use interface
• Good for HR teams transitioning from small businesses to mid-sized

Cons:

• Fewer advanced HR features than some other platforms
• Not as scalable as some solutions

9. OnPay

OnPay is an online payroll service provider that also offers tax calculation, benefits administration, time tracking, and other HR features. OnPay offers a user-friendly platform and transparent pricing that are primarily aimed at small businesses, with all features available on a single plan offering.

That’s where OnPay might fall short for enterprise organizations—its plan is offered at a base price plus a fee per employee, which means larger organizations will see their costs add up quickly.

And, with just one plan, larger organizations might find that OnPay just doesn’t offer as much flexibility and customizability as they need—and can find in other payroll platforms.

Key features for enterprise:

• Full-service payroll processing for full-time employees and contractors
• Self-service employee onboarding

Pros:

• Benefits administration with support from brokers across all 50 states
• Offers HR resources library and compliance support

Cons:

• Pricing model means high costs for larger organizations
• Less flexible and customizable than some other payroll platforms

10. UKG Pro

Formerly known as Ultimate Software and Kronos, UKG Pro is an HR software suite that offers payroll services, benefits administration, attendance tracking, and strong compliance features, all built for large workforces. However, it’s missing some key features that other platforms have that enterprise organizations often value in a payroll system.

For example, data isn’t unified in UKG Pro, which limits its ability to automate time-consuming administrative tasks.

UKG Pro is also costly to implement and maintain. It requires a full-time admin and takes as long as 20 months to fully implement. Then, it still charges for things like creating custom reports and approval workflows.

Key features for enterprise:

• Suite of HR tools
• Automatic tax calculations and compliance

Pros:

• Compliance support for large organizations
• Integrates well with other HR and enterprise tools

Cons:

• Implementation can be time-consuming
• Costly to run and maintain
• Can’t automate as many tasks and workflows as other platforms

11. Quickbooks Payroll

QuickBooks Payroll is part of the QuickBooks accounting software suite by Intuit. While historically focused on small businesses, QuickBooks has upgraded QuickBooks Payroll with enterprise features to attract larger organizations.

But Quickbooks is still primarily an accounting system used to pay employees—it doesn’t offer all-in-one HR features like onboarding, benefits administration, or attendance tracking. For scaling or enterprise organizations that want a true all-in-one, Quickbooks likely won’t be the best fit—they may want to seek out a more robust HR platform that can integrate with Quickbooks, if they still want to use Quickbooks for accounting.

Key features for enterprise:

• Direct link to QuickBooks accounting software
• Automatic payroll for salaried and hourly employees
• Easy tax filing for multi-state organizations

Pros:

• Strong brand recognition
• Convenient for companies already using QuickBooks for finance

Cons:

• Not an HR platform
• Not aimed toward enterprise organizations

12. Paylocity

Paylocity is a payroll provider that also offers HR tools like onboarding, time tracking, and compliance management. Among its payroll features are a popular employee self service portal, where employees can access pay stubs and view direct deposits and deductions. It also offers a custom workflow builder.

However, Paylocity doesn’t unify data across all its modules, so while you can build custom workflows, you can’t include any data from anywhere in your organization. You also can’t trigger events across HR, finance, or IT data.

And compared to some other payroll platforms, Paylocity’s reporting falls short—it doesn’t offer Excel functionality or cross-module reporting for HR, finance, and IT, and you can’t control what data users can access based on employee attributes.

Key features for enterprise:

• Employee self service features for checking direct deposits and deductions
• Custom workflow builder

Pros:

• Flexible software integrations with various HR and finance tools
• Automatically enforces federal, state, and local time and labor rules

Cons:

• Data isn’t unified across your organization
• Automations and reporting are limited compared to some other payroll providers

Enterprise vs. small business payroll system

Selecting a payroll system is not one-size-fits-all. Large companies demand a different level of functionality than small businesses. Here are a few key differences:

• Scalability: Payroll systems designed for small businesses can struggle with enterprise-level complexities like multiple pay groups, diverse deductions, and large-scale benefits administration.
• Customization: Enterprises often need payroll solutions that offer advanced customization for unique pay rules, multi-state tax filing, and specialized time tracking requirements.
• Compliance: Large corporations need to manage intricate regulatory environments. Enterprise HR software typically includes automated updates for new labor laws, so their payroll taxes and taxes filed remain accurate at all times.
• Cost: While small businesses might prefer a simpler, more budget-friendly payroll provider, larger enterprises may invest in premium software to handle extensive payroll management demands.

How to choose payroll software for large companies

When selecting the best payroll software for a large organization, consider the following factors:

Global payroll capabilities

If your business operates across borders, make sure your payroll system has robust global compliance and multi-currency payroll processing features. Automatic payroll for international teams can be a game-changer.

Automation features

Look for payroll software that automates everything from time tracking to tax calculations. Software can automate processes like tax filing and direct deposit, reducing manual tasks for your HR staff.

Integration capabilities

Seek out a payroll solution that offers integrations with your existing accounting software, time and attendance systems, or other HR software. Your payroll provider should excel at bridging different platforms together for smoother payroll processes.

Data security

Enterprises handle massive amounts of personal data. Make sure your payroll provider prioritizes data protection through secure servers, encryption, and strict compliance with privacy regulations.

Customer support and training

Rolling out new payroll software to a large workforce can be challenging. Look for vendors that offer in-depth onboarding, a mobile app, and ongoing training to help your HR staff and payroll administrators.

Easily manage your large company’s payroll with Rippling

If you want to maximize HR’s impact with enterprise HR and payroll software that can manage your day-to-day operations at scale—and help drive strategic outcomes for your business as a whole—you need Rippling.

Rippling Payroll is intuitive, easy to use, and has a 100% error-free guarantee on every pay run. It also offers 600+ integrations, automatic and accurate tax registration and filing, and a dedicated mobile app where your employees can view their W-2s and paystubs, submit expenses directly, and more. With Rippling, you can: 

• Pay employees and contractors in the same platform
•  Manage time and attendance natively 
• Run unlimited off-cycle pay runs at no extra cost 
• Set up multiple pay schedules, pay rates, and pay types in just a few clicks 
• Add recurring reimbursements (like cell phone payments, gym memberships, etc.) that are automatically paid out every pay period, monthly, or at whatever interval you choose
• Automatically calculate prorated pay runs for new or promoted employees 
• Manage all currency conversions, including payroll adjustments 
• Automatically calculate overtime for every country 
• Make changes after submitting payroll

FAQs on payroll systems for large companies

Which type of payroll system would be best suited for a large enterprise?

A payroll system with advanced payroll processing capabilities, multi-jurisdictional compliance, and strong benefits administration is ideal for large enterprises. Rippling is a common choice due to its unified data model, scalable platform, and automatic payroll features.

Which software is mostly used for payroll?

Many types of software are used for payroll, including standalone payroll processing platforms, as well as all-in-one HR suites that include payroll features. The software you choose should depend on your business needs.

What is the best accounting software for large businesses?

There are multiple choices for accounting software in the enterprise space—such as Oracle or NetSuite. Many large organizations integrate QuickBooks or another accounting software directly with their payroll or HR platform. This helps synchronize tax calculations, payroll reports, and deductions with your broader financial data.

How do I run payroll efficiently for a large workforce?

To run payroll smoothly, you’ll want payroll software that can manage payroll seamlessly across departments and locations, offer direct deposit, handle tax filing, and provide employee self service features. Look for a platform that offers online payroll tools to streamline running payroll tasks for large companies.

This blog is based on information available to Rippling as of February 17, 2025.

Disclaimer: Rippling and its affiliates do not provide tax, accounting, or legal advice. This material has been prepared for informational purposes only, and is not intended to provide or be relied on for tax, accounting, or legal advice. You should consult your own tax, accounting, and legal advisors before engaging in any related activities or transactions.