Ever tried calculating staff salaries manually? It starts off simple until leave requests, tax deductions, pension rules, and last-minute changes pile up by month-end. That’s when errors happen and suddenly, payroll becomes a full-time headache. A payroll software is built to solve exactly that.
It handles PAYE, NHF, pensions, and biometric attendance like it’s second nature. Whether you are processing salaries or managing multiple currency pays, it keeps everything clean, compliant, and easy to track.
In this guide, we’ll walk you through:
The best payroll software solutions in Nigeria
Key features to compare before you choose one
Why more HR teams are switching to automated, cloud-based systems
Let’s help you find a payroll solution that does the heavy lifting while your next payroll cycle sneaks up again.
Let’s look at some of the most trusted payroll software tools Nigerian businesses are using today:
A cloud-first payroll and HR platform, eHRX is explicitly designed for Nigerian businesses. It is a PAN african solution that handles it all. From PAYE, pensions, NHF, NSITF, and ITF deductions, you get full automation with built-in statutory compliance.
Key features:
Biometric attendance
sync
Payroll approval workflows
Employee self-service for payslips and tax slips
Seamless support for contractors, interns, and full-time
staff
Multi-currency support for remote teams
Integrated
HR modules for leave,
appraisals, and asset tracking
Best for: Companies that want a complete HR + payroll suite without worrying about
compliance.
Pricing
Custom plan based on features and company size (contact for quote)
A payroll tool developed for Nigerian SMEs. Offers basic HR support alongside tax compliance and salary automation.
Pros
Supports automated PAYE, pensions, and tax filing
Simple, clean dashboard for fast adoption
Built-in salary advance and employee benefits
options
Cons
Limited HR features beyond payroll
Self-service functions are basic.
Pricing
Free for the first 6 months
From ₦3,000/month after trial, plus transfer and payroll
run fees
Popular among businesses with hybrid or remote teams. Workpay offers full payroll automation, leave tracking, and employee records management.
Pros
Strong remote team support
Time tracking, attendance, and onboarding tools
included.
Cross-border compliance support
Cons
Premium pricing
Feature-heavy UI may be overwhelming for smaller
teams.
Pricing
Starts from $300/month per employee
Contractor plans start at $40/month.
Built with Nigerian startups in mind, SalarioPay offers affordable payroll processing and statutory deductions.
Pros
Affordable, transparent pricing
Supports PAYE, pension remittance, and bulk payments
Basic payroll reporting included
Cons
Limited HR functionality
No international payroll support
Pricing
Free plan for payroll
₦300 per employee for pension/tax
Admin access: ₦2,000/month
Geared towards enterprises across Africa, PaySpace offers high-level payroll security, auditing, and analytics.
Pros
Suitable for multi-country payroll operations
Built-in compliance and audit-ready reporting
Secure cloud infrastructure
Cons
Requires onboarding support for setup
Best suited for large organisations
Pricing
Custom quote only (no public pricing)
Ideal for small teams that want to test payroll automation. Offers a basic free version with optional upgrades.
Pros
Freemium access to basic payroll tools
Includes Nigerian compliance features
Easy to set up for new businesses
Cons
Key features locked behind a paywall
Limited HR capabilities
Pricing
Basic version free
Paid features available on request
A trusted name globally, Sage offers payroll modules tailored for the Nigerian market with leave tracking and staff profiles.
Pros
Strong local tax support
Integrates well with Sage accounting tools
Role-based access and employee portals
Cons
Setup can be technical.
No upfront pricing
Pricing - available on request
Want a software to manage people and pay together? That’s HR and payroll software.
It combines employee data, hiring, performance tracking, and salary processing. With an integrated platform, you can handle:
Employee onboarding and records
Recruitment and appraisals
Time-off tracking and attendance
Performance reviews
Payroll calculations and payslip generation
This differs from payroll-only tools, which focus on wage calculations, tax deductions and disbursement. Here is a quick comparison:
| Feature | HR + Payroll Software | Payroll-Only Tools |
| Recruitment & Onboarding | Yes | No |
| Employee Data Management | Yes | Limited |
| Leave & Attendance Tracking | Yes | No |
| Appraisal & Performance | Yes | No |
| Salary & Tax Processing | Yes | Yes |
| Payslip Generation | Yes | Yes |
| Employee Self-Service | Yes | Rarely |
Some of the popular HR+Payroll software are:
eHRX by Ekklaya – Full-suite platform built for local laws
Sage HR & Payroll – Combines HRMS and payroll
Zoho People + Zoho Payroll – Modular, works well together
PrimePayroll – Nigerian-friendly with HR add-ons
Doing payroll processing is an important step, and it must be done right. Here is how to prepare payroll in Nigeria to keep your business compliant and your team paid on time.
Before processing any salary, make sure these foundations are in place:
Register with local authorities such as
the Federal Inland Revenue Service (FIRS), NSITF,
PENCOM, and ITF.
Create a payroll policy that defines
pay cycles, benefits, deductions, and approval
workflows.
Gather accurate employee data,
including job titles, bank details, employment type
(permanent, contract, or ad hoc), and tax IDs.
Track time and staff attendance through attendance management software systems.
Once your setup’s ready, it’s time to calculate pay.
Calculate gross salary based on role or
hours.
Apply mandatory deductions:
PAYE (Pay As You Earn): income tax deducted monthly.
NHF (National Housing Fund): 2.5% of basic salary.
NSITF: contribution to the Social Insurance Trust Fund.
Pension: employee (8%) and employer (10%) contributions.
ITF: 1% of annual payroll for eligible companies.
Payroll doesn’t end after the money goes out.
Send payslips to every employee.
Remit deductions to FIRS, pension
managers, NHF, etc.
File monthly reports (like PAYE
schedules).
Keep records for audits and internal tracking.
What seems like an easy payment ly a lot of work. An intuitive software like eHRX by Ekklaya software can heautomateing these calculations.
Picking the right payroll software means aligning the tool with your company’s structure, workforce, and compliance responsibilities. Below are the key factors to consider when investing in one -
Business Size: A five-person startup won’t need the same features as a company with 500 staff across multiple branches. Check your needs before buying in.
Industry-Specific Needs: Don’t mindlessly purchase the most popular software. Some tools work better for certain sectors. Some don’t. If you're in construction, retail, or the NGO space, check if the software supports grant-based payment or project-based payroll.
Remote Work Support: Cloud access matters. Your team should be able to process payroll or view payslips anytime, from anywhere.
Budget: Some tools charge monthly, others ask for a one-time fee. Look at what's included before you decide.
Compliance: Ensure the payroll software adheres to Nigerian labour and tax laws.
Yes, free payroll tools do exist in Nigeria. But like most things free, there’s a catch. The free payroll software either offers basic automation features, user limitations or minimal support.
If you’re a small business with less than 20 employees, a free HR payroll software can help you test the waters.
Here are some options worth considering -
Designed for Nigerian small businesses, SalarioPay offers a free plan for teams of up to 20 staff.
NotchHR
NotchHR’s free tier covers core HR tools and payroll for smaller teams. You can process salaries, manage leave, and track attendance.
Payroll4Free
More old-school, this is a desktop-based payroll calculator. It’s free forever but lacks cloud access, integration, or Nigerian compliance features. Best suited for small teams that are comfortable with manual setups.
This is exactly what it sounds like: an Excel-based payroll template. There are no monthly or per-employee fees - just download and use.
While not entirely free, PrimePayroll offers a freemium model with basic features available at no cost. You’ll need to upgrade for automation, tax filing, or larger teams.
Creating payslips manually is risky. One missed deduction or miscalculation can trigger fines, employee distrust, or even tax audits. That’s why choosing the right payslip processing software in Nigeria is necessary.
While looking for the best options, here’s what a reliable payslip tool must offer:
Gross and net salary breakdown
PAYE, NHF, and pension deductions (based on Nigerian
laws)
Multi-level pay structures for ad hoc, contract, and
temporary staff
Automated tax calculations
E-file or digital archive
for each employee
Employee dashboards to download or view payslips
securely.
Audit trails and compliance logs
Now, let’s look at the top payroll computer software options available in Nigeria:
Built for businesses that can’t afford payroll mistakes, eHRX by Ekklavya is the best payroll software in Nigeria.
It auto-generates detailed payslips after every pay run—no templates, no toggling. Each slip reflects statutory deductions, loans, bonuses, and benefits. You can even set custom pay grades, automate pension and PAYE calculations, and give staff secure access to download their slips, anytime. Plus, it’s entirely cloud-based and designed to scale.
Bento brings clarity to payroll. Payslips are clean, fully compliant, and automatically sent to staff after each cycle. It adjusts in real-time for tax changes and offers built-in employee dashboards.
A 100% cloud software, PaySpace Africa is built for larger businesses like MNCs. Payslips are detailed and compliant, with strong data encryption and reporting tools for finance teams.
Workpay simplifies payroll across teams and time zones. Payslips include every deduction, bonus, or allowance, all mapped clearly. You also get automated reports, staff self-service, and role-based permissions.
eHRX by ekklaya is the best payroll processing software in Nigeria. It comes with intuitive tools for tax compliance, employee management, and automated calculations, making it ideal for businesses of all sizes.
If the headcount of your employees is high and you need speedy calculations compliant with Nigerian tax laws, then investing in payroll software is vital.