Top 5 Payroll Software and Companies in Nigeria

In this guide, you will discover the best payroll software and companies in Nigeria for small businesses and enterprises. I will show you how payroll systems, management tools, templates, and top payroll companies simplify payroll accounting.

Payroll in Nigeria shouldn’t feel like a math test at night, but it’s a huge pain for most business owners. The endless formulas, sudden changes, and all the “where’s my money?” calls.

It’s not that you’re a bad businessperson. Just that, you’ve had to use tools that weren’t made for the way things work in Nigeria.

Are you fed up with spreadsheets that mess up housing, tax headaches, and last-minute stress? Join the club! It’s not about how much you try, but how you do it!

You should totally get payroll software made for Nigeria. The best solutions take care of everything, like figuring out paychecks, overtime, and extra money. No tricks, just smart local tech to make payroll easy.

Are you ready to get software that saves you time and stress? Let’s find the top options for Nigerian businesses: fast, legal, and made for Nigeria.

Definition of a Payroll Software

Payroll software is a digital tool to make paying people easier, like calculating salaries, figuring out taxes, making payslips, and keeping everything straight, all while following Nigerian rules.

Seriously, it’ll boost how much you can do.

Okay, let’s get one thing straight: payroll software and a payroll system aren’t the same. Here’s my take:

• Software is your tool.
• The system is all about how you use it: your team, your methods, the rules, and the schedule.

For instance:

• You could use Platoon, Sage Payroll, or Zoho Payroll as tool.
• Here’s how the system works: paychecks go out on the 25th, team leads marks attendance, HR loads the info, finance checks it, and then they send it in.

Do you see the difference? One is the tool. The other thing makes the tool work.

If your system’s not strong, payroll will fail, no matter how good the software is, in my experience. If you have an excellent system, your payroll will run smoothly, even with basic software.

The real takeaway is this: software helps the system; it doesn’t take over. Get them both right, and you’ll avoid trouble, gain your team’s confidence, and stay on track.

Features of the Best Payroll Software in Nigeria

1. Automated Salary Calculation: The best software makes you enjoy an accurate, consistent payroll every cycle.

2. PAYE Tax & Pension Compliance: Auto-applies current FIRS tax brackets, PENCOM rates, NSITF, and ITF, with reminders for remittance deadlines. 

3. Payslip Generation: It creates professional, downloadable payslips that are branded, itemized, and mobile-friendly.

4. Integration with Accounting Systems: Syncs seamlessly with tools like QuickBooks, Zoho Books, or Sage, so payroll entries flow into your books automatically and closes the loop between HR and finance. 

5. Employee Self-Service Portals: Staff log in to view payslips, update personal details, or request leave, reducing HR bottlenecks. 

6. Custom Payroll Templates for SMEs: Pre-built, Nigerian-optimized templates for common structures, startups, retail, and agencies, so you’re not starting from scratch. Flexible enough to add transport, housing, or hazard allowances without coding or Excel chaos.

Importance of Payroll Software for Business Types in Nigeria

For Small Businesses (Between 1 and 10 staffs)

• Manual payroll eats 5-10 hours/month of the time you don’t have
• Software culminates affordable insurance. (Some tools start at ₦5,000/month.)
• Builds credibility with clean payslips and timely payments

For Startups (Scaling, 10–50 staffs)

• Need role-based access (HR vs Finance vs Admin)
• Must integrate with accounting tools (QuickBooks, Zoho Books)
• Software becomes your compliance backbone, especially for funding or audits

Large Corporations (50+ staff)

• Operating Manually is totally impossible
• Need: multi-branch support, bulk processing, audit logs, API integrations
• Using software isn’t optional; it’s operational infrastructure
• Delayed or incorrect payroll causes staff unrest, regulatory risk and reputational damage

If it doesn’t do these, you haven’t found the right software:

• It auto-calculates PAYE using current FIRS tax tables
• Deduct & track PENCOM, NSITF, ITF , with remittance reminders
• It also generate Nigerian-style payslips (with breakdown: basic, allowance, deduction, net)
• Store records securely for 6+ years (audit requirement)
• It syncs with Nigerian banks (GTB, Zenith, Kuda, Opay, UBA) for bulk salary payments
• Allow employee self-service. 

 Why Nigerian Businesses Need Payroll Software

• Compliance: So you never miss a statutory requirement again.
• Accuracy: Eliminates human error in salary calculations, allowances, and net pay.
• Time-saving: Replaces manual Excel templates with one-click payroll runs, freeing you for actual business growth.
• Data Security: Stores encrypted, audit-ready records for 6+ years; no more misplaced files during PENCOM visits.

Payroll Software vs Payroll Companies in Nigeria

When do you choose payroll software? What are the criteria you observe that make you pick software? This would guide you better 

Go with payroll software if you want to:

• Own the process, i.e., you run payroll, tweak settings to your satisfaction, and have unlimited access to data.
• Lock in cost no matter how many staff you add. Pay a flat monthly or annual fee depending on their business model.
• Move fast, run payroll the same day, and generate reports on demand. It is best for startups scaling fast, SMEs with structure, and founders who want hands-on control.

 Outsource to a Payroll Company If:

• You’re solo or under 5 staff with zero HR capacity
•  You’d rather pay a fee than learn a system
•  Compliance scares you, and you want someone to “handle it.”
•  Your payroll structure is simple. It is the best for micro-businesses, freelancers with staff, and founders that wish to focus purely on sales/service.

	Payroll Software	Payroll Company
Control	You own the data. You are in control	Limited, you hand over, they execute
Cost	Fixed monthly fee scales with you	Per-employee fee adds up
Speed	Instant runs and on-demand reports	Wait for their schedule
Compliance Risk	On you, but their tools guide you	on them, but verify their track record
Flexibility	Add allowances, bonuses, changes anytime	Changes means emails, delays, possible extra fee

 Top Payroll Companies in Nigeria

• PayDay 
• Remita Payroll 
• BreatheHR Nigeria 
• Grey 
• PayrollServe Africa 

Top Payroll Software in Nigeria 2025

1) Platoon (Built for Real Life)

Platoon remains the best payroll software built in Nigeria for small businesses at the moment.

It is very easy to set up (can be done in minutes). Even if you’re not that “techy.” You can add departments, invite staff, and schedule payroll yourself

You can get quick customer support (over chats or calls). They have free trials where your business can use their full payroll system for FREE for 2 months. You only pay small fees when you actually send salary (like bank transfer charges).

Then after those 2 free months, you can start to pay their official monthly price with no surprises nor hidden charges.

Platoon costs between ₦5,000 and ₦15,000 per month, and I think that is very fair for small and growing businesses.

Platoon is perfect for startups, growing SMEs, and founders who want peace of mind and happy staff without having an HR team.

2) Sage Payroll (Built for Structure)

When I first used Sage Payroll, I knew its way simpler than doing payroll manually. Isn’t it annoying to deal with salaries and taxes each month? Sage takes the pressure off of you. It runs itself.

I’m a big fan of how it manages all the Nigerian tax stuff. You don’t need to worry or lose sleep about following the rules. You enter the data, and Sage will do the rest.

Plus, the best part is: Sage does more than just numbers. It ensures timely payments, clean records, and everyone gets paid properly, no headaches.

This will cut down on our stress, reduce errors, and free us up to concentrate on actual work, rather than spreadsheets.

If payroll ever gives you grief, check out Sage Payroll. You’ll love how simple, and stress-free payroll becomes, like, right away.

•  Built for complex payrolls, multi-branch, union rules, and full compliance.
• Works better if you already use Sage accounting.
• Audit-proof and It is priced at about ₦25,000/month. It is best with an HR/finance person on deck, and it is perfect for established businesses (20+ staff) or Sage users scaling up.

3) QuickBooks Payroll

QuickBooks Payroll is another of the most popular software in Nigeria.

Payroll is a real headache, couple with calculating salaries, taxes, and sending out those payslips on time.

You won’t have to worry about that stuff with QuickBooks Payroll. The software handles the hard work, so you don’t have to.

I like that QuickBooks Payroll makes things easy. Just put in your info, and the system handles paychecks, taxes, and pay stubs automatically.

Are you worried about complying? No longer here. This software keeps your payroll on track so you don’t have to check everything twice.

QuickBooks also makes it easy to stay organized. You ensure outstanding records, readily have your payslips, and pay your employees on schedule.

Basically, you’ll make fewer mistakes, avoid arguments, and build more trust with your team.

You may also want to check the list of best alternatives to QuickBooks accounting software.

QuickBooks Payroll can save you from payroll stress and time-wasting. It’ll really streamline your payroll process. It’ll be less stressful, and your business will run more smoothly.

• It is suitable for remote teams, mobile apps, and self-service and offers decent automation.
• It is priced at about ₦15,000/month, plus your QBO subscription (₦25,000+). It is perfect for businesses already using QuickBooks and okay with doing a little manual compliance tweaking.

4) Xero + Payroll Add-on

Your Xero account brings it all together. Setting up your employees makes payroll super easy. Everything to do with your pay is automatic, so you won’t waste time figuring it all out.

Here’s the cool thing: Your payroll data links directly with your accounting, which means your books stay clean and updated without extra effort.

You’re also in charge of your own records. Everything’s in order: clean payslips, reports ready when you want them, and staff paid on time. It helps you trust people and avoid trouble.

If you’re struggling with payroll, Xero’s Payroll add-on is a good option. It’ll save you stress, cut down on mistakes, and let you focus on growing your business, not messing with spreadsheets. Making payroll will be simple, fast, and not stressful.

• Beautiful dashboard, real-time data, and strong bank feeds. 
• It is priced at ₦12,000/month + Xero base (~₦13,500). Total: ~₦25,500+. It is perfect for creative agencies, tech startups, or global-facing SMEs who value design and data.

5) Zoho Payroll

I bet you find managing payroll annoying too. Zoho Payroll does all the heavy lifting, making things super simple. This is a digital tool that does all the work for you, calculating your pay, deductions, and pay stubs automatically.

What do I really like? Zoho handles all the Nigerian tax stuff, like PAYE, PENCOM, and ITF, so you don’t have to worry. Your employees can log in whenever to see their pay and salary info.

You can also connect Zoho to your bank to pay salaries directly. So, your team always gets paid on schedule. You can pay your entire team in just a few clicks, which beats using spreadsheets by a mile.

Zoho gives you reminders, so you don’t have to worry about remembering stuff like when your paychecks are ready or when taxes are due. It plays well with other Zoho apps if you’re already using them.

Seriously, to save time, avoid payroll errors, and keep your team happy, check out Zoho Payroll. Just try it; you might love it!

• It is built-in Nigerian compliance, PAYE, etc. Self-service portal for staff. Mobile app included.
• It grows with you, from 5 staff to 500, without having to change tools.
• It is priced at about ₦8,000/month. It is perfect for Nigerian SMEs who want simplicity, compliance, and room to grow without breaking the bank.

Comparison Table of Payroll Software Solutions In Nigeria

FEATURES	PLATOON PAYROLL	ZOHO PAYROLL	SAGE PAYROLL	QUICKBOOKS PAYROLL	XERO + PAYROLL
Best For	Startups & SMEs wanting Nigerian-built, simple, free-to-try payroll	Growing SMEs that needs  affordable, scalable tool	Large SMEs or corps with complex payroll	Businesses already using QuickBooks Online	Agencies, global teams, design lovers
Nigeria compliance	Auto-handles PENCOM, ITF, and NSITF. Built for local law	Built-in Nigerian tax & pension logic	Deep compliance, audit-ready	Needs manual check for PENCOM/NSITF	Global tool, Nigerian rules not native
Ease of Use	Super simple, set up in minutes; staff get self-service access	Clean interface, easy for non-tech users	Complex, best with HR/finance team	Smooth if you know QBO	Sleek, but payroll feels “added on.”
Pricing	FREE for 2 months (pay only transaction fees) → then ~₦5k–₦15k/month	₦8,000 per month	₦25,000 per month	₦15,000/month (add-on) + QBO fee	₦12,000 (add-on) + Xero base (~₦13.5k)
Employee Self-Service	Yes, staff can view payslips, history, deductions anytime	Yes	Yes	Yes	Yes
Support	Nigerian team, available across platforms.	Mostly guide or forums,	Professional, but formal & corporate	Global support, not always Nigeria time.	Decent, but not Nigeria-focused
Ideal for	Want to test risk-free, need trust and transparency.	Want value and compliance	Have 20+ staff, or use Sage already	Already on QuickBooks & okay with tweaking compliance	Value design, data, and global features

 Payroll Management Best Practices in Nigeria

• Stay compliant by automating PENCOM, PAYE, and NSITF deductions using Nigerian-tailored software.  
• Training of your HR and basic tool mastery . This cuts errors and saves audit stress.  
•  Run quarterly payroll audits within to discover your mistakes before FIRS or staff do.  
•  Using standardized templates ensures consistency, especially before migrating to full software.

How to Choose the Right Payroll System in Nigeria

Here’s what I look for in payroll software; it’ll save you a major headache down the road.

1. Size of the company.

The size of your company is a big deal when choosing payroll software. If you’re new with a few employees, it’s different from a huge company.

If you’re a small business, I’d suggest checking out Platoon, they’re competitive and easy. They keep it simple so you don’t get lost in stuff you don’t need.

2. Money

Money is usually the main issue for us Nigerian business owners. People buy the cheap stuff and end up paying more to get it working right.

So, I learned this: don’t focus on the monthly price. Factor in setup fees, training costs, and any extra charges for features you’ll need.

You can get a basic Zoho plan that’s good for small teams, but the bigger versions are pricey.

3. We need to connect things.

You have accounting, HR, and banking software already, right? Your payroll software needs to work with these other programs.

I learned the hard way when I chose software that didn’t talk to my accounting system. Total disaster!

Ensure these systems work together, so you don’t have to type everything in yourself.

4. Local versus global.

The payroll software I mentioned on this list all works for Nigerian companies. They get how taxes, pensions, and banking work for us. You can use Sage or Zoho, be sure they follow Nigerian laws.

I always say, stick local unless you need to go international – it’s a lot easier to deal with the rules.

The bottom line? Take the time to test these four factors. Your future self will thank you!

Conclusion:

The use of manual payroll is costing you time, trust, and sleep. Why then stress yourself? So sit back and run the business while the software runs the payroll.

Future of Payroll Software in Nigeria

By the end of this year, 60%+ of Nigerian SMEs will leave Excel for cloud payroll. Free trials (like Platoon’s 2-month beta) will drive adoption. Compliance will be 100% automated. 

 Cloud-Based is Now Standard: Cloud tools like Platoon let you run payroll from anywhere.

 AI & Fintech Will Quietly Take Over Soon: Tools that auto-flag or predict require no admin. Fintech will handle salary payments, pensions, and even loans inside the same platform.

 Local Players Will Rise Fast

FAQs (Frequently Asked Questions)