Payroll compliance feels complicated when every deduction lives in a different portal, spreadsheet or email thread. The easiest way to stay in control is to turn the month into a repeatable process with clear owners, review points and proof of every action.
This guide gives Kenyan employers a practical routine for 2026. It is designed for finance teams, HR teams and business owners who want to pay people accurately and remain ready for questions from employees, auditors and regulators.
1. Confirm employee changes before calculation
Start with the facts that can change gross pay or deductions. Confirm new employees, exits, unpaid leave, overtime, bonuses, commissions, benefits, salary changes, bank details and statutory identifiers. Ask managers to approve changes before they enter payroll.
A dated cutoff protects everyone. It gives payroll enough time to check unusual entries and gives managers a clear point after which late adjustments move to the next cycle.
2. Calculate PAYE using current rules
PAYE is deducted from employment income and remitted by the employer. The Kenya Revenue Authority states that the return and payment are due by the ninth day of the following month. Your review should confirm taxable benefits, allowable deductions, personal relief and any valid exemption before payroll is approved.
Review the current PAYE guidance from KRA whenever rates or treatment may have changed.
3. Review NSSF, SHIF and Housing Levy separately
Do not treat statutory deductions as one combined number. Each obligation has its own basis, employer responsibility and remittance trail.
- NSSF: check the current contribution year and the applicable lower and upper earnings limits. NSSF published a specific employer notice for Year 4 rates in 2026.
- SHIF: validate the contribution against gross salary and confirm every eligible employee is correctly registered.
- Affordable Housing Levy: KRA describes an employee contribution of 1.5 percent of gross pay with a matching 1.5 percent employer contribution.
Keep calculation reports separate from payment evidence. This makes reconciliation faster when a portal total differs from the payroll total.
4. Use a maker and checker review
The person preparing payroll should not be the only person approving it. A second reviewer should compare headcount, total gross pay, total deductions and net pay against the prior month. Large movements need a written explanation.
Good payroll control is not about adding more work. It is about making the important checks visible before money leaves the business.
5. Reconcile payment and preserve evidence
After approval, compare the final payroll register with the bank or wallet payment file. Record rejected payments and corrections. Store the approved register, statutory schedules, portal acknowledgements, payment confirmations and payslip delivery record together for the month.
A simple monthly close
- Lock approved employee changes.
- Run payroll and review exceptions.
- Complete independent approval.
- Release salaries and resolve rejected payments.
- File and remit statutory obligations on time.
- Archive reports, receipts and approvals.
MyAccurate Payroll brings employee changes, calculations, approvals, payslips, statutory reports and audit history into one controlled workflow. That gives your team a clear answer when someone asks what was paid, why it changed and who approved it.
