How to run payroll in Nigeria: a monthly step-by-step checklist

Good payroll isn't about working harder each month — it's about running the same disciplined sequence every time. Here's the monthly checklist that keeps a Nigerian payroll accurate, compliant and defensible.

1. Prepare the inputs

Before you run anything, make sure new joiners are added and assigned a salary structure, leavers are processed, and any approved leave, loans or one-off items for the period are in. Confirm everyone who should be paid has an active bank account.

2. Run and read the pre-run checks

Start the run and read the pre-run checks first. They flag the things that quietly break a payroll — a missing bank account, a zero net pay, an unusually large change versus last month. Resolve the high-severity ones before you go further.

3. Review the variance report

Once it computes, compare the draft against last month. Every meaningful change should have a reason — a new hire, a raise, a proration. Anything unexplained is worth a second look before you commit.

The variance report is the cheapest insurance in payroll. Two minutes here saves a month of corrections.

4. Approve and lock

When you're satisfied, approve the run. This locks the period and makes the figures final. Best practice — and good governance — is that the person who ran payroll is not the person who approves it.

5. Pay the team

• Create the payment batch from the approved run
• Have a second person approve it (maker-checker)
• Download the NIBSS file and upload it to your bank
• Reconcile each line as paid, returned or failed

6. Remit the statutory deductions

Generate the remittances and pay them by their deadlines: pension by the 7th of the next month, PAYE by the 10th, NHF by month-end. Record each payment reference as you go.

7. Close the month

Finally, run the rollover to close the period and open the next. The discipline of closing cleanly is what makes next month's run boring — which, in payroll, is exactly what you want.