Payday should be exciting. But unfortunately, for most small business owners, it's the opposite. A single miscalculation in payments or tax filings, and the business loses employee trust and invites penalties.
Tired of chasing spreadsheets, payslips, and tax deadlines every month?
But what if we told you that you can automate all the payday headaches and save atleast 30% or more of your time?
This is exactly what modern payroll software for small business is designed to do. From accurate salary calculations to automated tax filings, it takes the pressure off your plate and gives you full control over every payout.
In this guide, we will explore the best payroll accounting software in Nigeria that can help small startups and businesses like yours to save HR’s valuable time, reduce the chances of payroll errors, and pay your team with confidence.
Finding payroll software in Nigeria isn't just about cutting down effort. It's about staying compliant, building trust, and growing sustainably.
Following is a curated list of the top 7 best payroll software for small business in Nigeria -
1.eHRX by EklavyaBuilt specifically for Nigerian businesses, eHRX simplifies everything from salary processing to statutory remittance.
Ease of Use: Clean interface, simple onboarding.
Compliance: Handles Nigerian tax laws and payslips automatically.
Scalability: Ideal for both small teams and growing businesses.
Price: contact for custom quotes.
Pros:
Local support team
Integration with Nigerian banks and job boards
Statutory reports (PENCOM, NSITF, PAYE)
2. GustoPopular among startups for ease of setup and automation.
Ease of Use: Very beginner-friendly
Compliance: Handles US taxes (limited Nigeria-specific features)
Scalability: Better for teams under 50
Price: $40 base + $6 per employee
Pros:
Automatic tax filing and employee self-service portal
Time-off and benefits tracking
Cons:
No Nigerian tax automation
Pricing adds up with features
3. Wave PayrollSimple, affordable, and great for basic payroll processing.
Ease of Use: Straightforward and clean UI
Compliance: Limited to North America
Scalability: Designed for micro-businesses
Price: $20 base + $6/employee (self-service); $40 + $6 (tax service states)
Pros:
Integrates with Wave accounting
Transparent pricing
Cons:
Not Nigeria-friendly
Lacks HR functions
4. OnPayCombines payroll, benefits, and HR support.
Ease of Use: Guided onboarding
Compliance: US-based compliance
Scalability: Can grow with your team
Price: $40 base + $6/employee
Pros:
Multistate payroll support
Excellent customer service
Cons:
US-centric tax handling
Requires manual tweaks for Nigerian laws
5. QuickBooks PayrollBest known for seamless accounting integration, QuickBooks Payroll is ideal for businesses already using QuickBooks Online.
Ease of Use: Perfect for users familiar with QuickBooks
Compliance: Strong US compliance, but customisable for Nigerian workflows
Scalability: Works well for small to mid-sized businesses
Price: Starts at $45/month + $5 per employee
Pros:
Full integration with QuickBooks Online
Same-day direct deposit
Automated tax filings and year-end prep
Mobile app for payroll on the go
Cons:
Premium features are only in higher-tier plans
Less ideal if you're not already using QuickBooks
6. ADP RUNBuilt for scaling businesses, ADP RUN offers flexible, enterprise-grade features.
Ease of Use: Professional setup and support
Compliance: Multi-state and global compliance tools
Scalability: Designed to grow with your business
Price: Custom quote only
Pros:
End-to-end HR and payroll automation
Mobile payroll app
Access to HR professionals and onboarding tools
Cons:
Not transparent with pricing
Learning curve for small teams
Extra fees for some features
7. Remita PayrollA Nigerian-made payroll solution trusted by banks, universities, and public institutions.
Ease of Use: Built for compliance with Nigerian regulations
Compliance: Includes IPPIS, tax, pension, and NHF processing
Scalability: Handles large-scale payroll across sectors
Price: On request
Pros:
Built-in compliance with Nigerian law
Used by the government and private sector firms
Good local customer service
Cons:
Enterprise-level setup
May be overkill for small startups
Sage PayrollLast but not least, Sage is a trusted name in accounting and business management. Sage Payroll is particularly suitable for SMEs looking for reliability and local support.
Ease of Use: Desktop and cloud options available
Compliance: Local tax laws and statutory filing handled
Scalability: Good fit for growing SMEs
Price: Based on modules selected (quote required)
Pros:
Established user base in Nigeria
Integration with Sage Business Cloud
Strong local presence and support
Cons:
Interface may feel outdated
Initial setup can be technical
A modern payroll application software handles more than just payments. Here are the core features you should expect:
Employee Management: Centralised employee records with secure access.
Salary Computation: Automatic gross-to-net salary calculations.
Payslip Generation: Auto-generated, downloadable slips.
Statutory Compliance: PAYE, NSITF, NHF, and pension deductions handled for you.
Additional modules that may be included:
Leave and Attendance Tracking: Syncs with punch-in tools or mobile check-ins.
Timesheets and Shift Scheduling: Useful for hourly or contract workers.
Benefits Management: Handles health plans, bonuses, and reimbursements.
Integration with Accounting Tools: Syncs with platforms like QuickBooks, Xero, or ERP systems.
Still processing payroll manually? Here's what you're missing out on:
Fewer Errors, More Accuracy: Auto-calculations reduce costly mistakes on tax filings and salaries.
Save Hours Every Month: On average, small business owners spend 5–10 hours a month handling payroll. With automation, you can reclaim that time to focus on sales, operations, or growing your team.
Legal Compliance: Good software keeps up with local regulations, reducing audit risk.
Better Employee Trust: Timely, transparent payments boost morale and reduce attrition.
Smarter Insights: Access reports to see payroll trends, team costs, and tax obligations.
Scalable Processes: Easily add new employees, contractors, or pay types without disrupting your system.
Remote Payroll Access: Many cloud-based systems allow access anytime, from anywhere.
Automated Tax Filings: Some tools auto-calculate and submit tax forms to the relevant authorities.
Scale Without Overhead: Whether you are onboarding two or 20 new hires, your system adjusts without needing a bigger HR team.
Absolutely. Using payroll software for small business can help you save both time and money.
When done manually, payroll often requires hiring admin support or outsourcing to an external firm. Either way, you are adding headcount or external billing.
Let’s say you run payroll manually for a 10-person team.
You spend 10+ hours a month double-checking calculations, preparing payslips, and making statutory deductions. That’s over 120 hours a year.
Now, assume admin time is worth ₦5,000/hour.
So, you are spending ₦5000*120 = ₦600,000/year just managing payroll.
A modern employee payroll application software is an investment that pays off well in terms of -
Reduced payroll errors
Avoidance of duplicate entries
Less risk of penalties from late or inaccurate tax filings.
Minimal employee disputes over salaries
Faster payroll cycle with less back and forth.
Lower year-end costs due to clean and export-ready reports.
Less dependency on external consultants or agencies.
Controlled administrative overheads even as your team grows.
The average cost of payroll software can range between $20 to $399 per month, excluding additional fees. Below is a general estimate for small businesses -
| Team Size | Estimated Monthly Cost Range |
| 1–10 employees | $20–$100 (or ₦10,000–₦50,000) |
| 10–50 employees | $50–$300 (or ₦25,000–₦150,000) |
If you consider outsourcing platforms or recruiting a payroll specialist, it will come at a higher cost than the automation models.
The payroll cost quoted above is decided based on factors like the popularity of the provider, features, and number of employees in your team. To understand better, there are three main pricing models to choose from:
Flat-Rate Pricing: A fixed monthly fee regardless of team size. It does not matter whether you have 25 employees or 50, the price structure remains fixed.
Per-Employee Pricing: A base monthly fee plus a charge per employee.
Tired Pricing: When the model is categorised into tiers (like basic, standard, and premium) with different pricing as per features and customisation.
Besides, there are some other hidden fees like:
One-time setup fees
Year-end filing charges (W-2s, 1099s, etc.)
Add-ons like premium support, time and attendance tracking, employee data analytics and reporting features.
Integrations with CRM, ERP, and other systems.
While free payroll tools exist, they often come with limitations (user caps, no tax support, etc.). For long-term ease, investing in paid payroll application software usually pays off.
eHRX by Ekklavya is the best payroll software for small businesses in Nigeria.
Investing in payroll accounting software as a small business might seem doubtful, but it can bring you time and money savings by automating payroll processes, integrating HR functions, and providing robust security features