How to run payroll in Kenya

A business KRA PIN is not the same as being registered as an employer for PAYE — that is a separate obligation added on iTax before the first payroll run, not after. NSSF and SHIF each need their own employer registration too, each with their own number, and the Affordable Housing Levy rides on the PAYE registration rather than needing one of its own.

Do all of this before you promise anyone a pay date. A registration that is still pending on payday does not delay the obligation to deduct and remit correctly — it just means you are doing it while also chasing paperwork.

Each employee needs their own KRA PIN, national ID number, and bank or M-Pesa details on file before their first payslip — not gathered after the fact when a return will not file. An NSSF number an employee already holds from a previous employer should be recorded rather than treated as a fresh registration.

Statutory deadlines count from when pay is due, not from whenever it actually goes out. Every deduction below is due to its own body by the 9th of the month following the one it was deducted in, regardless of which day employees were actually paid that month.

A pay date that drifts from the 25th one month to the 3rd the next does not just look disorganised to employees — it eats into the window you have to get everything else below done correctly.

Running payroll produces the payslips and the figures. Filing submits the statutory returns built from those figures. Paying settles what is owed with KRA, NSSF and SHIF. Treating these as one action is how a business ends up having filed correctly but not paid — which still counts as non-compliant.

Check each one actually landed before moving to the next: a payslip issued, a return accepted (not just submitted — iTax and the fund portals can reject a return after submission), and a payment confirmed against the right reference.

After the first run, the cycle is the same every month: run payroll on the fixed pay date, issue payslips, file that month's PAYE, NSSF and SHIF returns, pay each body by the 9th of the following month, and keep the records — payslips, returns, proof of payment — for the period the law requires.

The month this breaks down is usually the one where someone is on leave, an employee joined mid-month, or a deadline lands on a weekend. None of those change the deadline; they just mean the work has to happen a few days earlier than the calendar suggests.

This is a process guide, not tax advice, and the filing obligation stays with you as the employer. See the compliance page for what each deduction is and which return it ends up on, and the PAYE calculator for the actual figures.