How to Pay Your Staff’s Salary Automatically with Payrolls in Nigeria

If you’re running a business in Nigeria, whether it’s a small startup or a growing company, one thing you can’t avoid is paying salaries. Manually sending money to each staff member every month is not only stressful—it’s risky and time-consuming.

But here’s the good news: you can automate your salary payments with payroll software. That means your staff get paid on time and you save hours of stress.

In this guide, I’ll walk you through how to set it up. I’ll explain it in simple language for you—no tech jargon, no confusion. Let’s go!

Step 1: Understand What Payroll Software Does

Let’s start by clearing up what payroll software actually is.

Payroll software is a tool (usually an app or website) that helps you calculate, manage, and pay your employees’ salaries without you having to do it manually every month.

It does things like:

• Calculate salaries (based on hours worked or agreed monthly pay)
• Handle taxes and pension deductions (if needed)
• Send the money directly to your staff’s bank accounts
• Generate payslips
• Keep salary records

Think of payroll software like your own HR + accountant in one simple app.

Step 2: Choose a Payroll Software That Works in Nigeria

Not all payroll software is built for Nigerian businesses. So you need to pick one that:

• Supports Naira
• Connects with Nigerian banks
• Handles local taxes and pension rules

Popular Payroll Software in Nigeria:

1. Sage Payroll
2. SeamlessHR
3. BukkaHut Payroll
4. PayDay by Bento
5. QuickBooks Payroll (some features may be limited)

Let’s use SeamlessHR for this guide, as it’s Nigerian-based and beginner-friendly.

Step 3: Sign Up and Set Up Your Payroll Account

Now that you’ve chosen your software, go to their website and create an account.

Here’s what you’ll usually need:

• Company name
• Business email address
• Phone number
• Tax Identification Number (TIN) (optional, but good to have)
• Bank account details for salary payments

Once you’re signed up, the platform will give you access to a dashboard. This is where all the magic happens.

Step 4: Add Your Employees

Now, let’s load your staff into the system.

You’ll need their:

• Full name
• Email address or phone number
• Job title
• Monthly salary amount
• Bank account details (very important)
• Employment type (full-time, part-time, contract)

Most payroll platforms let you upload all your staff at once using an Excel sheet. Or you can enter them one by one.

Take your time here. Double-check bank account numbers to avoid payment issues later.

Step 5: Set Salary Structure and Payment Schedule

Now that your staff are added, you need to:

• Define how much each person earns
• Set the pay cycle (e.g. monthly, biweekly)
• Add any deductions (like pension, tax, or loan repayment)
• Include bonuses or commissions if needed

Example:

• Staff A earns ₦100,000 monthly
• Pension deduction: ₦8,000
• Tax: ₦5,000
• Net Pay: ₦87,000

Most payroll platforms will calculate these automatically once you enter the formula or rules. If not, they have customer support that can help you set it up.

Step 6: Connect Your Bank Account

To pay salaries automatically, you need to connect your business bank account to the payroll system.

This is safe, and most platforms work with major Nigerian banks like:

• GTBank
• Access Bank
• Zenith Bank
• First Bank
• UBA

Here’s what will happen:

• You authorize the payroll platform to make salary payments on your behalf.
• They will deduct the total salary amount from your bank account and send it to your staff’s bank accounts on payday.

You’ll usually have to sign a short mandate or confirm with your bank via email or online banking.

Step 7: Do a Test Run (Very Important)

Before you go live, do a test with 1 or 2 staff to make sure:

• Bank details are correct
• Payments go through smoothly
• Deductions and net pay are accurate

Ask your staff if they received the right amount and if the payslip looks okay.

This step helps you avoid mistakes with the full team.

Step 8: Go Live and Automate

Once your test run works, you can now activate automatic payroll.

This means:

• Every month (or week), the system will calculate salaries, apply deductions, and pay your staff without you lifting a finger.
• You’ll get a notification before it pays (in case you want to pause or adjust anything).

Most systems also generate payslips and send them to your staff by email.

Step 9: Keep Records for Future Reference

After every payroll cycle, make sure you:

• Download salary reports
• Save payment receipts
• Keep payslips (in case of any staff complaints)

These records are useful for tax filings, business loans, and auditing.

Bonus Tips:

• Train someone on your team to use the payroll software, so it doesn’t all fall on you.
• Update salaries or deductions whenever there are changes (like promotions or bonuses).
• Use payroll to calculate taxes like PAYE, pension, and NHF—this helps you stay compliant with Nigerian law.

My Advice: Let Payroll Work for You

Running a business is hard. Payroll should not make it harder.

With automatic salary payments:

• You reduce errors
• Save hours every month
• Keep your team happy
• Look more professional

If you’re serious about growing your business in Nigeria, investing in a payroll system is one of the smartest moves you can make.