Payroll software for small businesses in the Philippines

Running payroll is a time-consuming task for a small business. There’s more to it than just remunerating employees – you also need to calculate taxes, manage mandatory contributions, generate payslips and meet local regulations for BIR, SSS, DOLE (and more).

Using payroll software can make these important tasks easier by automating key processes so everything is more accurate and compliant, which saves time and month-end headaches. In this guide, we’ll look at what payroll software is, list some key features, and then compare five of the best payroll software for small business owners in the Philippines.

What is payroll software for small businesses?

Payroll software is a digital tool that automates many of the critical tasks for sorting payroll, like salary calculations, tax withholding, government contributions, and payslip generation. Because compliance rules are strict and paperwork is repetitive, using payroll software lightens the admin burden and creates more accurate, consistent records with fewer costly errors.

It helps you stay compliant with key local requirements, including:

• BIR withholding tax - calculates the correct tax to withhold each payroll period so your filings are accurate.
• SSS contributions - handles employer and employee SSS contribution shares so that monthly remittances are correct.
• PhilHealth contributions - applies the correct percentage rates and updates them when new guidelines take effect.
• Pag-IBG contributions - make sure deductions are consistent and prevent issues with underpayments.
• DOLE record-keeping rules - maintains proper payroll logs and payslips so everything is compliant and above board during inspections.

Why Filipino small businesses need payroll software

Startups and micro businesses often rely on spreadsheets and outsourcing routine tasks to accountants when starting out. While this might work initially, it becomes more difficult to keep on top of everything as the business grows.

Payroll software helps by:

• Reducing manual calculations and errors in tax, SS, PhilHealth, and PAG-IBG contributions
• Supporting compliance with DOLE rules and BIR reporting
• Keeping a clear audit trail for all your payslips and employee records
• Scaling easier as your headcount increases, without adding more admin work

Key features to look for in small business payroll software

When choosing payroll software, Filipino MSMEs should focus on features that prevent compliance mistakes and reduce admin, with an eye on scaling and growing easier later on. The essentials include:

• Payroll automation - automates salary calculations and recurring payroll runs each cycle with minimal manual input.
• Local compliance automation - applies the correct rules automatically and updates rates when guidelines change.
• HR integrations - connect payroll with employee records so everything flows into one system without having to input details twice.
• Employee self-service - reduces the burden on HR by using a service with employee portals. These allow staff to view their payslips, apply for annual leave, and update their personal information.
• Local payout and banking support - generates bank files for BDO, MayBank (and others) to make domestic salary disbursements easier and faster.
• Global-ready workflows - supports multi-currency reporting or contractor classifications, and can work alongside tools like Wise Business for international payouts.

Best payroll software for small businesses in the Philippines

Based on these core features, here are five top payroll software tools for small businesses in the Philippines, starting with an overview of what each offers.

Now, let’s look at each provider in more detail.

Sprout Payroll

Sprout is a cloud-based workforce platform purpose-built for the Philippines. It automates salary calculations, government contributions, and report generation, helping MSMEs reduce processing time by 90% and stay compliant with all the key local regulations⁴.

Sprout is regularly updated with the latest tax tables and statutory rules, which is useful if you don’t have dedicated payroll staff.

Sprout offers three tiers that it says are tailored for “every business”⁴:

• Sprout Starter - a lightweight package for startups and micro businesses that need the basics like timekeeping and government compliance.
• Sprout Payroll - the core software for MSMEs that want to automate key tasks. It supports 32 pay rates and quickly generates government forms.
• Payroll Professional Services - an outsourced payroll service

The payroll solutions are part of Sprout’s broader HR solutions that also include ‘Talent Management’ and ‘Employee Retention’⁵, so if you’re looking at using one connected platform for everything, it might be a good option.

Payroll Hero

Payroll Hero is another platform designed for Philippine businesses, with a focus on payroll and time tracking. It automates gross and net pay calculations (and other key tasks) for local compliance, generates all the required government forms and offers exportable payroll and attendance reports in PDF or Excel⁶.

One of its key strengths is built-in time and attendance tools – there are features like selfie clock-ins, scheduling, attendance resolution, and GPS tracking⁶. This might make it a good fit for small businesses with schedules that change or that work on multiple sites (including remotely).

Other compelling features include⁶:

• Bank file integration with MayBank, HSBC and others
• Support for statutory rules like night differential and 13-month pay
• Allowances and benefits tracking to keep company benefits organised
• HRIS tools, including leave management and organizational charts

GreatDay HR

GreatDay HR is a workforce and payroll platform, again curated for the local Philippine market. It brings all the important tasks – payroll, attendance, leave, and employee records – into one system, reducing the errors that often plague small businesses that rely on separate tools. The platform is also fully compliant with Philippine tax rules, including TRAIN Law, with automatic updates for these⁸.

Other essentials on GreatDay HR include⁸:

• Multi-country tax, including Singapore, Malaysia, Thailand, and Hong Kong.
• Customisable payroll cycles, including weekly, fortnightly, and monthly schedules
• Mobile payslips with password protection and optional printed copies
• HRIS tools covering leave, performance, and 201 file management
• Biometric attendance recording (geo tagging and geo tracking)⁹

Because GreatDay HR recommends a minimum of around 20 employees⁷, it’s likely a stronger fit for growing small businesses rather than startups and micro teams.

QuickBooks Payroll

If you’re after a broader, global solution, QuickBooks Payroll is a popular option that pairs payroll with accounting and HR tools, all within one platform¹⁰. Because it’s focused primarily on US tax rules and compliance, it doesn’t have direct support for Philippine requirements like BIR withholding or Pag-IBIG. However, it might still appeal to MSMEs that already use QuickBooks for accounting or operate internationally.

Key features include:

• Automated payroll runs with scheduled pay cycles
• Integrated time tracking that lets you sync hours directly into payroll
• HR and benefits tools, including onboarding and time-off management
• Deep integration with QuickBooks Online for accounting and expense tracking

QuickBooks Payroll will likely best serve Philippine businesses already in the QuickBooks ecosystem, especially those with US operations. You’ll need to register it as a CAS (Computerised Accounting System) to the BIR to use it legally¹¹.

JeonSoft

JoenSoft is slightly different to the other tools listed because it offers two payroll options: an on-premise system (JeonSoft Payroll Suite) and a cloud-based platform (Payroll.PH). Both are built for built for Philippine business and local regulations, including BIR rules and TRAIN Law.

With the on-premise solution, all your data is stored locally, which might appeal if security is a top priority. It combines payroll, time and attendance, and HRIS into one system, with support for biometrics, bundy clock integrations, and employee self-service for payslips and tax forms¹². Payroll.PH, the cloud version, offers the same 3-in-1 setup, but with the flexibility of secure web access from any device¹³.

Overall, JeonSoft is ideal for MSMEs that need a locally compliant payroll system with strong attendance integrations. And the option of either more control with an on-premise setup or the versatility of a cloud platform.

Challenges with handling payroll across borders

Running payroll in countries across borders for workers outside the Philippines makes the process more complex. Small businesses that rely on freelancers overseas, for example, are often unprepared for the additional burden and admin.

Even with good software, you can run into issues like:

• Different tax and labor rules - every country has its own payroll laws and employee entitlements, which makes it easy to miss something important.
• Higher transfer and banking fees - cross-border payments often come with steep charges that hit your margins, especially when paying smaller amounts or multiple people.
• Slow or inconsistent payment timelines - international transfers can take longer to settle, usually a few days, which can result in late salary payments and disgruntled staff.
• Compliance risks - misclassifying overseas workers or missing a local requirement can lead to back payments or even penalties and legal issues.
• Multiple currencies - paying staff or contractors in different currencies means constantly dealing with fluctuating exchange rates, which are likely to have markups with traditional banks.

Wise Business: Simplify your global payroll

Wise Business works alongside any payroll tools you choose by handling all your cross-border payments. Payroll software sorts compliance, tax rules, and contributions for the Philippines, then

Wise lets you pay remote workers and other employees abroad in their local currency. Always at the mid-market rate, with no hidden fees or markups.

• Send from PHP with both Instapay and Pesonet.
• Fast and secure payments to 140+ countries with no exchange rate markups.
• Always get the mid-market rate with transparent conversion fees starting from 0.57%.
• Set up Batch Payments to make up to 1,000 payments in a single click.

➡️Start Paying Overseas Invoices with Wise Business

Wise Pilipinas Inc. is regulated by the Bangko Sentral ng Pilipinas. You may visit the BSP website for more information about its regulatory framework and consumer protection policies. To reach Wise, visit help center here.

Sources:

1. Payroll Hero - Pricing
2. GreatDay HR - Pricing
3. QuickBooks - Payroll Pricing
4. Sprout PH - Payroll management
5. Sprout PH - Home page
6. Payroll Hero - Philippine payroll
7. GreatDay HR - Home page
8. GreatDay HR - Payroll & E-payslip
9. GreatDay HR - Mobile app
10. QuickBooks - Run payroll
11. QuickBooks - Registering QuickBooks to BIR Philippines as a CAS
12. JeonSoft - JeonSoft Payroll Suite
13. JeonSoft - Payroll.PH