Kenya VAT3, eTIMS and payroll contributions

# Kenya VAT3, eTIMS and payroll contributions

Rates and codes. Install the Kenya set from Taxes > Tax codes. It has standard rated 16%, standard rated capital goods 16%, zero-rated supplies, zero-rated exports, exempt supplies, and supplies outside the scope of VAT. Verify the rates with your tax office.

The VAT3 worksheet. Open Tax and payroll: Africa > Kenya. Choose the period and press Show the worksheet. It lists standard-rated sales, zero-rated sales, exempt sales, purchases, output VAT, input VAT and the VAT payable. The layout is a draft: check it against the template on the portal before you copy anything.

eTIMS. Every invoice must be sent through eTIMS. After you send an invoice, record its eTIMS invoice number and control code on the Kenya tab against that invoice. The CSV button lists the period's issued invoices and marks each one recorded or missing, so you can see what still needs to go through. The CSV is a draft layout; check it against the portal template.

NSSF, SHIF and the housing levy. Each scheme has an employee rate, an employer rate, an earnings ceiling and optional tiers. They are all entered by you. Save them, tick that you have checked them, pick a posted pay run, and press Contribution report or CSV file.

What the pack doesn't cover. Income tax, PAYE and the actual eTIMS submission are not done here. Pop Books calculates no income tax and sends nothing to the Kenya Revenue Authority.

Verify with your tax office. Last reviewed 2026-11-06.