Payroll Tax Changes in Kenya 2025

The world of finance and regulation in Kenya is constantly shifting, and the recent changes from the Finance Act, 2025, along with the landmark High Court ruling on the Social Health Insurance Fund (SHIF), prove just how quickly things can change.

At HRBOX Africa, our goal is to take the stress out of this process. We believe that managing payroll and statutory deductions should be straightforward. We've been working hard to ensure our platform is fully updated to handle these changes, so you can focus on what you do best: running your business.

Navigating a New Era of Statutory Deductions

The most significant changes we’ve seen are in statutory deductions, particularly with the recent court ruling.

National Social Security Fund (NSSF): We've seamlessly integrated the new NSSF rates, effective from February 2025, into our system. Our platform automatically handles the new tiered contributions, ensuring accurate deductions and timely remittances by the 9th of each month.
Affordable Housing Levy (AHL): Both employers and employees must contribute 1.5% of their gross salary to the AHL. Our software is configured to handle this deduction accurately, making compliance effortless.
Social Health Insurance Fund (SHIF): This is the most crucial update. The High Court's ruling on June 23, 2025, declared the 2.75% SHIF deduction unconstitutional. This decision has an immediate and direct impact on your payroll. We've taken swift action to ensure our platform reflects this legal development:
- SHIF deductions have been removed from our system.
- We are actively advising our users to stop all SHIF deductions immediately.
- We are preparing for potential refund mechanisms for past deductions and will continue to monitor the situation for any government guidance or appeals.

Mandatory Tax Reliefs and New Benefit Limits

The Finance Act, 2025, now makes it a legal requirement for employers to automatically apply all eligible PAYE tax reliefs. This includes the Personal Relief (Kshs.2,400 per month) and Insurance Relief (up to Kshs.5,000 per month). Our platform handles this automatically, eliminating the risk of manual errors.

In addition, the new law brings welcome changes to how certain employee benefits are taxed. The tax-free limit for non-cash benefits has increased to Kshs.60,000 annually, and tax-deductible pension contributions have risen to Kshs.360,000 per year. HRBOX’s flexible system allows you to easily track and apply these new rules, ensuring your payroll accurately reflects all taxable and non-taxable benefits.

Stiff Penalties and Tax Amnesty

With increased penalties for late filing and payments, the cost of non-compliance has never been higher. This is where automation becomes your greatest asset. HRBOX helps you avoid these costly mistakes by automating calculations, integrating with statutory portals, and providing real-time updates on legislative changes. We also encourage you to use the KRA’s tax amnesty, which runs until June 30, 2025, to clear any outstanding obligations.

The recent legal changes in Kenya highlight the need for a reliable, up-to-date, and legally compliant payroll system. At HRBOX Africa, we are dedicated to providing you with a solution that goes beyond simple processing. We offer a partnership built on trust and accuracy, so you can focus on your core business, confident that your payroll is in full compliance with the law.

Don’t let these legislative changes expose your business to risk. Partner with a solution that’s built for Africa’s unique and evolving landscape.

Ready to simplify your payroll and ensure full compliance?

Schedule a personalized demo with our team today and discover how HRBOX Africa can empower your business to thrive.

Gloria Nekesa-Communication Associate