Best Payroll System in Kenya? What Payroll Software Must Get Right in 2026

Payroll in Kenya is a moving target. Rates and ceilings change by law, and a spreadsheet that was right last year can be wrong this month. Payroll software earns its fee by keeping up so you don't have to.

What Kenyan payroll must calculate (2026)

• SHIF (health): 2.75% of gross pay, with a KSh 300 minimum
• Affordable Housing Levy: 1.5% of gross pay, matched by the employer
• NSSF: Tier I and Tier II contributions. The Tier II upper limit rose to KSh 108,000 in February 2026, so the maximum employee contribution is now KSh 6,480 a month, matched by the employer
• PAYE: five bands from 10% to 35%, with KSh 2,400 monthly personal relief. SHIF, the Housing Levy and NSSF are deducted before PAYE is calculated
• Payslips, the P9 at year end, and the monthly returns to KRA, SHA and NSSF

These are the rates as published at the time of writing. Check KRA and NSSF notices before each new financial year, or use software that updates them for you.

How to choose payroll software

• Does it update statutory rates automatically, and how fast after a change?
• Can it generate the KRA, SHA and NSSF files in the right format?
• Does it handle casuals, commissions, allowances and loans?
• Can staff see their payslips on their phones?
• Does it link to your accounting software?

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