How to run payroll for a small business in Nigeria

Payroll is one of the few jobs in a small business that has to be right every single time. Get it wrong and you lose trust with your team, or end up owing penalties. Here is a simple monthly routine.

Before your first payroll

• Keep one record per employee: name, role, start date, bank details, salary and tax ID.
• Write down each person's pay structure: basic, housing, transport and other allowances.
• Register for PAYE with your state's revenue service, and set up pension with a PFA for eligible staff.

Every month

• Update changes: new joiners, leavers, raises, unpaid leave and overtime.
• Work out gross pay for each person.
• Take off deductions: pension, NHF where it applies, and PAYE under the 2026 bands.
• Review the totals, then pay net salaries.
• Send payslips that show every figure.
• Remit PAYE, pension and other deductions by their deadlines.

Common mistakes

• Still using the old CRA after it was abolished in 2026.
• Forgetting to adjust for mid-month joiners and leavers.
• Paying salaries but remitting deductions late.

Payroll is a checklist. The trick is to never skip a step.

Hand the checklist over

Profynix prepares payroll before payday: changes, deductions and payslips, ready for review. You approve, and nobody is paid without you. Staff see their payslips in their own portal.