Best HR and Payroll Systems for Mid-Sized Companies in the Philippines

Running a mid-sized company in the Philippines has its rewards. A skilled workforce, expanding teams, growing revenue, a large customer base, and stability in operations. 

However, this growth comes with increasing demands without a proper HR payroll system Philippines in place. Manual computation of statutory deductions like SSS, PhilHealth, and Pag-IBIG, preparing BIR tax forms, and multiple income cadres can cause payment errors and inconsistencies. As such, employee dissatisfaction and risk of compliance fines and penalties can arise.

This is why choosing the right HR and payroll system Philippines is crucial for your business. You want to ensure that the payroll provider you choose is tailored to the specific needs of your business and aligns with Department of Labor and Employment guidelines and other relevant regulations.

In this article, we’ll walk you through the best HR payroll system Philippines in the market for mid-sized companies, the unique features of each provider, and how you can make the best choice for your business.

Benefits of an integrated HRIS and payroll software

Having an integrated HRIS and payroll provider Philippines is non-negotiable if you’re looking to manage or scale your mid-sized company without compromising on your finances or HR management. 

Read next: How Integrated HR Software Streamlines BPO Operations

Accurate statutory contribution and tax calculations 

The Philippines operates complex labour codes and tax laws. Minor errors in statutory contributions or tax calculations can result in unhappy employees or worse compliance fines. An integrated HRIS and payroll system ensures that statutory contributions like SSS and Pag-IBIG are accurately and promptly deducted based on the salary scale. Taxes are also calculated & deducted accurately using such software.

Automated updates when rates change

Government rates and deduction rates are subject to regular updates and amendments. Your business may encounter compliance issues if you’re unaware of these rate changes. Integrated HRIS and most payroll provider Philippines provide automatic synchronization, which reflects on your dashboard whenever official rates change.

Faster payroll processing across multiple branches 

An integrated HRIS and payroll provider Philippines provides a streamlined process for disbursing payments to employees. This is vital for large companies with multiple branches, thus ensuring that workers receive payment promptly regardless of their location. This increases employee satisfaction and promotes an efficient work culture.

Self-service for payslips, leave, and claims 

An ideal HR payroll system Philippines comes with self-service features that help employees stay in the loop regarding the organizational payment structure and deduction of payroll taxes. Employees can view their payslips and apply for leave from the payroll software, thus reducing dependency on HR.

Better visibility through centralized HR analytics 

HR and payroll systems in the Philippines take away the guesswork by giving your business solid, centralized data for decision-making. With centralized HR analytics, you can monitor patterns and trends in employee retention, attendance, overtime costs, statutory compliance, and payroll accuracy. This level of visibility helps you identify bottlenecks, forecast labor costs, and make data-driven decisions that improve both employee experience and workplace efficiency.

Why Omni HR is the Ideal HR Payroll System for Philippine Companies 

The ideal HR payroll system Philippine businesses need isn't the one with the most features or aesthetics. It is the one whose features suit your business needs and is built for the complex labour landscape of the Philippines. Here's why Omni HR checks these boxes:

Automated SSS, PhilHealth, Pag-IBIG, and BIR withholding tax 

Manually computing statutory contributions like SSS, PhilHealth, and Pag-IBIG heightens the risk of errors and can result in overpayment, underpayment, and compliance issues. 

As a specialized payroll provider Philippines companies trust, Omni HR mitigates this risk by automatically making deductions based on local labour regulations, approved deduction rates, employees’ salary range, and age. 

With localized payroll automation and country-specific compliance built in, you get instant payroll reports and centralized records that integrate seamlessly with your time-tracking and accounting tools. This eliminates manual computing, increases compliance, and reduces payroll processing time by up to 50%. 

"Payroll calculations that used to take three to five working days can now be done in half the time with Omni." 
— Tengku Mohaizad, Group Head of HR Asia at Inspire Brands Asia

Multi-country payroll support for SEA expansion 

Whether you are paying salaries or reimbursements in Philippine pesos or other currencies, Omni has you covered with our multi-country payroll feature supporting 190+ countries and 10+ languages. 

Employees get paid in their preferred local currency, with local compliance and accurate deductions, saving them service fees on currency conversions. This streamlined HR payroll system Philippines companies use makes it easier to attract diverse talent across Southeast Asia and scale confidently into new markets.

“Omni's highly adaptable and customizable HRIS empowers us to easily manage our distributed workforce across existing and future countries of operation. The intuitive interface and automated workflows streamline our processes, saving us time and minimizing errors.”
— Lovely Tan, Philippines Country Head of People at Qashier

Employee self-service and mobile experience 

Omni HR has an intuitive user interface on the web and mobile app, and a self-service portal that non-technical employees can navigate easily. Employees can edit basic information, update bank details, submit time-off requests, and access their payslips, all from their phones. 

With automated calculations and customizable approval workflows, leave requests automatically route to the appropriate manager, and both employees and managers can view real-time balances without going through HR. Managers can also approve requests with a single click, eliminating delays and paperwork.

"Once I get a notification, I can just approve from the app. I don't even have to log into the website – straight away I click approve, and it's done." 
— Wenna Lee, HR Manager at IHRP

Complete HRIS: leave, performance, attendance, recruitment 

Omni HR is a comprehensive HR and payroll system Philippines businesses rely on. From recruitment and onboarding with digital document collection and e-signatures, down to employee information like leave tracking, performance management with 360 feedback, and attendance with time-tracking integrations, Omni ensures you always have a ready update. 

Our unified platform provides secure, centralized employee records with custom fields for role-specific or country-specific data. This single source of truth improves data accuracy, frees your HR team from mundane repetitive tasks, and helps them focus on strategic people management.

Advanced reporting & analytics 

With Omni HR, you can generate detailed reports or custom templates in minutes instead of hours. You have access to custom dashboards for headcount, leave, and payroll data, plus analytics for performance, attrition, and workforce planning, all export-ready for audit and decision-making.

Access to real-time graphs and data-driven insights that help you identify trends, address employee burnout or disengagement proactively, and make informed decisions that drive measurable results.

Local support for Philippine customers 

As a trusted payroll provider Philippines organizations choose, Omni offers local support from dedicated teams in APAC time zones to help Philippine companies navigate the intricacies of labor laws, payroll, hiring, employee management, and statutory deductions. 

Unlike legacy providers where you raise a ticket and wait for a response, our implementation and account managers are available in your time zone, ready to customize the system to your unique needs and respond quickly as your business grows.

“The support that comes from the Omni team is unmatched. As a company that is quickly growing, there are constantly new features and functions that we require to serve our mission. Having access to a quick and dedicated chat with Omni's team members in our same time zone helps us make the changes we need to get the most out of our HRIS." 
— Trevor Lim, Head of Operations at Capital Club

How to Choose the Right HR Payroll System Philippines 

When you want to choose the right HR payroll system Philippines for your business, you need to keep a few things in mind. They include:

SSS, PhilHealth, Pag-IBIG, BIR compliance automation 

The Philippine labour law takes these statutory contributions seriously, and you run the risk of compliance penalties in the event of miscalculations or errors.  Ensure that your HR payroll system in Philippines supports the automation of these deductions to reduce manual errors and processing time. Also, look out for the automation of 13th-month pay, holiday pay, overtime pay, night differential, and other mandated allowances. The right system should handle country-specific compliance calculations automatically, giving you instant payroll reports and maintaining centralized records that are always audit-ready. 

Check if the payroll provider Philippines you’re considering automatically updates their system when the statutory rate changes. Can it generate BIR-compliant reports with one click? These capabilities separate basic payroll software from truly localized solutions built for Philippine compliance requirements.

Multi-country payroll

If you’re planning to expand, the right payroll provider in Philippines should have multi-country payroll features that let you create and schedule your pay run in other currencies. This will help you attract and retain talent if you’re looking to expand to other geographical areas within SEA. Look for a system that supports multiple countries with localized compliance for each region, so you can pay employees in different regions with accurate statutory deductions.

Assess if the system can handle multiple currencies and country-specific labour regulations simultaneously. The best HR and payroll system Philippines companies choose will scale with your expansion plans without requiring you to switch providers halfway, or add expensive integrations.

Required HRIS modules

When choosing an HR and payroll system in the Philippines, start by ensuring it includes the core HRIS modules your team needs for daily operations, specifically leave management, performance management, and attendance tracking. 

These modules allow HR teams to automate leave requests and approvals, maintain accurate attendance data synced directly to payroll, and monitor employee performance without jumping between spreadsheets or separate tools. For mid-sized Philippine companies, these modules also play a major role in payroll accuracy: attendance data flows directly into payroll calculations, leave balances update automatically based on DOLE requirements, and performance records with 360° feedback help support compensation decisions. 

A unified HR payroll system Philippines that combines these modules in one platform reduces manual errors, strengthens compliance, and gives you a more complete view of your workforce. Look for systems that offer customizable leave policies with APAC-specific leave types (service incentive leave, parental leave, TOIL) and real-time balance visibility for both employees and managers.

Learn more: Leave and Attendance Management Systems in APAC

Self-service and mobile features 

Self-service and mobile features improve transparency and build trust, and decrease response times for on-the-go tasks. Hence, ensure that you look out for an HR payroll system Philippines that offers robust self-service capabilities accessible from any device. 

Using the self-service portal and mobile app, employees can update their personal details, submit time-off requests that automatically route through customizable approval workflows, view their payslips, check leave balances in real time, and navigate their personal dashboards, all without going through HR.

When your payroll provider Philippines includes mobile-first features, you empower your workforce to be more resourceful while reducing the administrative burden on your HR team. This is especially critical for companies with field staff, remote workers, or distributed teams across multiple locations.

Reporting and audit-readiness 

The right HR payroll system Philippines should provide detailed reports and analytics for tracking trends in retention, overtime costs, labor costs, and compliance status. Look for custom dashboards that let you monitor headcount, payroll data, performance metrics, and attrition rates with export-ready reports for audit and decision-making. 

Check for access to audit trails, which help you track changes and identify errors when they occur. This feature ensures that you have a system for proper reporting and documentation, both for your records and for compliance audits. The best system allows you to generate reports in minutes, with real-time graphs and data-driven insights that help you make proactive decisions.

Verify whether the HR and payroll system Philippines you’re evaluating charges additional fees for custom reports or data modifications. Some providers may impose these costs, while truly flexible systems include unlimited reporting configurations at no extra charge.

Pricing vs efficiency gains 

When possible, optimize for the best HR payroll system in the Philippines that gives you the highest return on investment per dollar. This doesn’t mean selecting the cheapest option; instead, prioritize a system that offers real value and remains cost-effective even as your mid-sized business grows. A solution that becomes too expensive or difficult to scale will erase the benefits you initially paid for.  

Omni tops the chart here, starting at just $3 per month per employee. With enterprise-ready features at mid-market pricing, paired with same-day local support, you get the scalability and customization of expensive legacy systems without the additional cost. 

Access my free ROI calculator now

Best HR and Payroll Systems for Mid-Sized Companies in the Philippines

1. Omni HR

Key features

• Automated statutory compliance: SSS, PhilHealth, Pag-IBIG, and BIR payroll calculations
• Full HRIS suite: leave, attendance, performance management, recruitment
• Multi-country payroll support for regional workforce expansion
• Advanced analytics and reporting for payroll, headcount, and compliance tracking

Pros

• Best for mid-sized companies with regional presence across APAC
• Strong local compliance expertise and in-platform statutory automation
• Highly responsive customer support, including onboarding and migration assistance
• Extensive educational content and resources (blogs, guides, webinars) for navigating PH and SEA employment regulations
• Workflow automation reduces manual payroll and HR processing

Cons

• May have limitations for highly complex or niche custom workflows, especially for organizations requiring extensive bespoke process design

Best for: Mid-sized companies that need reliable Philippine statutory compliance alongside scalable local and multi-country payroll and HR operations.

Pricing: Starts from $3 per employee per month. 

Find the perfect pricing plan for your budget

2. Sprout Solutions

Key Features

• Core payroll and HRIS modules
• Attendance and timekeeping tools
• Strong Philippine regulatory compliance coverage
• Add-ons for wellness, performance management, and compliance automation

Pros

• Detailed analytics and reporting
• Add-on modules for complex HR strategies

Cons

• The platform is best suited for larger enterprises with more HR resources
• Higher pricing, potentially excessive for small and mid-sized teams
• Some advanced features may be overkill for simpler HR needs

Best for: Large SMEs and enterprises needing deep, Philippines-only compliance with advanced HR modules.

Pricing: Starter plan begins at PHP 5,000/month for up to 10 employees.

3. PeopleHum

Key features

• Recruitment (ATS)
• Performance management
• Employee engagement tools
• HR analytics
• Payroll modules

Pros

• Simple and intuitive UI
• Strong customer support

Cons

• Onboarding and implementation can be complex
• Payroll localization depth varies depending on the country integration method
• Transparency features can result in broader employee data visibility, which may require careful permissions management

Best for: Organizations focused on talent lifecycle management and performance analytics, with payroll as a supporting function rather than the primary driver.

Pricing: Core plans start from approximately $2 per employee per month.

4. GreatDay HR

Key Features

• Attendance and time tracking
• Leave and scheduling management
• Payroll processing
• Mobile-first workforce platform
• Basic analytics

Pros

• Strong for distributed and on-the-go teams
• User-friendly mobile interface for frontline and shift workers
• Covers essential HR operations without heavy setup

Cons

• Limited flexibility for process customization
• May lack depth for advanced payroll compliance or multi-country expansion
• Cost structure can feel less competitive when scaling

Best for: Companies prioritizing mobile workforce management and simple HR workflows over complex payroll or compliance features.

Pricing: Starting from PHP 70 per day.

Choosing the Best HR Payroll System in the Philippines for Mid-Sized Teams

With the complexity of managing SSS, PhilHealth, Pag-IBIG, and BIR withholding tax, mid-sized companies in the Philippines need more than just a basic payroll app. 

While platforms like Sprout, peopleHum, GreatDay HR, and Qupus offer strong functionality, Omni HR stands out with our unified HR and payroll platform, multi-country support, and a scalable system designed for your fast-growing needs. Book a demo with our team today and see why Omni is the HR payroll system Philippines for you.

Frequently Asked Questions

1. What does an HR payroll system do in the Philippines?

An HR payroll system in the Philippines provides your business with a streamlined platform for managing employee data, onboarding documents, and monthly payroll. Beyond basic salary calculations, a comprehensive HR and payroll system Philippines automates statutory deductions (SSS, PhilHealth, Pag-IBIG, BIR), tracks attendance and leave, manages performance reviews, generates compliance-ready reports, and offers employee self-service portals. 

The right system integrates all these functions into one unified platform, reducing manual errors, ensuring regulatory compliance, and freeing your HR team to focus on strategic initiatives rather than administrative tasks.

2. Can Omni automate SSS, PhilHealth, Pag-IBIG, and BIR tax?

Yes, Omni automates the deduction of statutory contributions like SSS, PhilHealth, Pag-IBIG, and BIR tax based on local labour laws, approved deduction rates, employees' salary range, and age to ensure you stay compliant. Our system also automatically handles 13th-month pay calculations, holiday pay, overtime pay, and night differential. When government rates change, Omni updates automatically, so you never have to worry about outdated calculations or compliance penalties. As a specialized payroll provider Philippines companies trust, Omni reduces payroll processing time by up to 50% while maintaining 100% accuracy on statutory compliance.

3. Does Omni support multi-country payroll for regional teams?

Yes. Omni HR is the perfect payroll provider in the Philippines for mid-sized businesses with regional teams that disburse payments in multiple currencies. Our multi-country payroll feature supports 190+ countries and 10+ languages, allowing you to pay employees in HKD, SGD, MYR, PHP, and other local currencies with accurate statutory deductions for each region. 

Whether you're expanding across Southeast Asia or managing distributed teams, Omni's localized compliance engine ensures you meet country-specific labour regulations without switching providers or adding expensive integrations.

4. What's the difference between basic payroll software and an HRIS?

Basic payroll software differs from an HRIS in that it is specific for handling payments to employees, freelancers, or international contractors. An HR and payroll system Philippines with full HRIS capabilities is more encompassing as it includes both payroll processing and comprehensive HR management, such as leave tracking, performance management with 360° feedback, attendance monitoring, recruitment and onboarding, document management, workflow automation, and advanced analytics. 

For mid-sized Philippine companies, an integrated HRIS eliminates the need to juggle multiple systems: attendance data flows directly into payroll calculations, leave balances update automatically based on DOLE requirements, and all employee information lives in one centralized, audit-ready location. This integration reduces manual errors, strengthens compliance, and provides better visibility for strategic decision-making.

5. How much does Omni HR cost for Philippine companies?

Omni HR offers enterprise-ready features at mid-market pricing, starting at just $3 per month per employee. Unlike some providers that charge additional fees for custom reports, data modifications, or advanced features, Omni includes reporting configurations, local support from APAC-based teams, dedicated implementation and account managers, and access to our core HRIS modules at no extra cost. 

Use our free ROI calculator to see exactly how much time and money your company can save by switching to Omni.

6. Is Omni compliant with Philippine labor laws and DOLE requirements?

Absolutely. As a trusted HR payroll system Philippines built specifically for the APAC region, Omni is designed with Philippine labor law compliance at its core. We automatically handle all DOLE-mandated requirements, including service incentive leave calculations, 13th-month pay, statutory contributions (SSS, PhilHealth, Pag-IBIG), BIR withholding tax, holiday pay, overtime pay, and night differential. 

Our system updates when government rates change, ensuring you're always compliant. We also maintain comprehensive audit trails and generate BIR-compliant reports, so you're always prepared for audits and regulatory reviews.

7. Can employees access their payslips and leave balances on mobile?

Yes. Omni's mobile app (available on iOS and Android) empowers employees to access their information anytime, anywhere. Through the employee self-service portal, team members can view and download payslips, check real-time leave balances, submit time-off requests, update personal details, track attendance, and navigate their personal dashboards, all from their phones without going through HR. 

Managers can approve leave requests with a single click directly from the app, making Omni ideal for companies with field staff, remote workers, or distributed teams.

8. How long does it take to implement Omni HR?

Implementation timelines vary based on company size and complexity, but many mid-sized Philippine companies complete onboarding in just a few weeks. Omni HR provides dedicated implementation and account managers who guide you through every step: data migration, system configuration, employee enrollment, workflow setup, and team training. 

We offer templates for common processes, automated reminders about deadlines, and even handle tasks like uploading public holiday calendars for your locations. Unlike legacy systems, where you raise a ticket and wait 24-48 hours, Omni's award-winning support team is available in your time zone for assistance, ensuring a smooth transition with minimal disruption to your operations.

9. What integrations does Omni HR support?

Omni HR seamlessly integrates with your team's favorite work tools through plug-and-play connections. We offer bi-directional sync with Google Workspace, Microsoft Teams, and Slack (for leave approvals and notifications), time-tracking systems for automated attendance data, accounting software for payroll reconciliation, and integration with local government systems for compliance reporting. 

Our integration with calendar platforms means birthdays and work anniversaries automatically appear in team calendars, and leave schedules sync in real-time. These integrations eliminate double data entry, reduce manual errors, and ensure your entire tech stack works together efficiently.

Check out Omni’s growing integrations

10. What makes Omni HR different from other payroll providers in the Philippines?

Omni HR stands out as the leading HR payroll system Philippines mid-sized companies choose for several reasons:

• We're built specifically for APAC with deep Philippine compliance expertise and multi-country scalability, not adapted from Western systems.
• We offer same-day local support from dedicated teams in your time zone, not 24-48 hour ticket responses.
• We're a 5-time "Easiest to Use" award winner with an intuitive interface that requires minimal training.
• We provide enterprise-ready features (workflow automation, advanced analytics, 360° performance reviews) at mid-market pricing starting from $3/employee/month.
• We deliver measurable results: customers report 50% faster payroll processing, 20% reduction in attrition, and reports generated in minutes instead of 12 hours. Plus, our highly customizable platform adapts to your unique needs rather than forcing you into rigid workflows.

11. Can Omni handle different employment types (full-time, part-time, contractors)?

Yes. Omni's flexible HR and payroll system Philippines accommodates various employment arrangements, including full-time employees, part-time staff, freelancers, contractors, and international workers. Our system allows you to set up custom fields for role-specific or country-specific data, configure different pay schedules, apply appropriate statutory deductions based on employment type, and manage benefits eligibility accordingly. 

Whether you're paying monthly salaries to full-time staff or processing reimbursements for contractors in multiple currencies, Omni's unified platform handles it all while maintaining accurate records and compliance for each employment category.

12. What kind of reports can I generate with Omni?

Omni provides comprehensive reporting and analytics capabilities that transform hours of manual work into minutes of automated insight. Generate detailed reports on headcount trends, payroll costs, overtime expenses, leave utilization, attendance patterns, performance metrics, attrition rates, and compliance status. 

Create custom dashboards tailored to your specific needs or use preset templates for common reports. All reports are export-ready for audit purposes, board presentations, or strategic planning. Unlike some providers that charge fees for every custom report, Omni includes reporting configurations at no additional cost. Access real-time graphs and data-driven insights that help you identify burnout risks, forecast labor costs, and make proactive decisions that improve both employee experience and operational efficiency.