Automate PAYE, NSSF, SHA, NITA, and Housing Levy with a secure, multi-company payroll system built for Kenyan businesses, churches, and enterprises.
Purpose-built for Kenyan statutory compliance — from PAYE to Housing Levy, calculated accurately every month, across every company.
All Kenyan statutory deductions computed automatically and updated in line with KRA and regulatory changes — no manual intervention required.
Run payroll for multiple entities, subsidiaries, or client companies from a single admin account — with full data isolation per company.
Give employees a secure, dedicated portal to access their own payroll data — reducing HR overhead significantly.
Every statutory report and submission file needed for compliance — formatted exactly as required by each Kenyan authority.
A repeatable, audit-ready workflow — from employee setup to statutory submission.
Import employee records via CSV or add manually. Set salary structures, KRA PIN, tax relief, and statutory settings per employee.
Run payroll for the month in one click. PAYE, NSSF, SHIF, NITA, and Housing Levy are all calculated and verified automatically.
Produce payslips, P9A, P10A, and bank payment files. Review and approve before any payment or submission is made.
Export iTax-ready files and statutory schedules. Submit PAYE to KRA and contribution files to NSSF, SHA, and NITA directly.
BioTrack Payroll is updated in line with KRA and regulatory changes as they happen — so your payroll remains compliant without manual intervention. When NHIF became SHA, your system updated automatically.
Reduce HR overhead by giving employees direct access to their own payroll records. Completely separate login, completely separate session — isolated from all admin functions.
From churches and NGOs to manufacturers and multi-company groups across Kenya.
"BioTrack Payroll handles our PAYE and NSSF deductions without any manual intervention. When SHA replaced NHIF, the system updated automatically — we didn't have to change anything."
"We run payroll for three separate companies from one account. Each entity has its own reports, statutory settings, and payslips. The multi-company feature alone justified the entire investment."
"The employee portal reduced payslip-related HR queries by over 70%. Employees download their own payslips and P9A certificates directly. Our HR team now focuses on actual people work."
Each plan is scoped to your headcount, number of companies, and compliance requirements. Contact our team for a tailored quote.
We do not publish fixed pricing — every payroll implementation is scoped by headcount, number of entities, and selected features. Request a custom quote and our team will respond within 24 hours with a proposal tailored to your organisation.
Answers to the most common questions about PAYE, NSSF, SHIF, and how BioTrack Payroll handles compliance automatically.
BioTrack Payroll calculates PAYE using the current KRA tax bands and applies all applicable reliefs automatically — including personal relief (KES 28,800 per year), insurance relief (15% of premiums), and mortgage interest relief. The system is updated whenever KRA publishes new tax bands or rates, so your calculations remain accurate without any manual changes.
Under the NSSF Act 2013, contributions are split into two tiers. Tier I covers earnings up to the Lower Earnings Limit (LEL), with both employee and employer contributing 6%. Tier II covers earnings between the LEL and the Upper Earnings Limit (UEL), also at 6% each side. BioTrack Payroll calculates both tiers automatically and generates contribution schedules formatted for NSSF CSV upload.
Yes. From October 2024, NHIF was replaced by SHIF (Social Health Insurance Fund) under the Social Health Authority (SHA). BioTrack Payroll was updated automatically at the transition — if you were an existing customer, nothing changed on your end. SHIF deductions are calculated at the current SHA-prescribed rate and appear in all payslips, reports, and deduction schedules.
Yes. BioTrack Payroll generates iTax-ready PAYE return files that can be uploaded directly to KRA's iTax portal. No manual data entry is required. The system also generates P9A and P10A annual tax certificates for each employee, which are available for download by both HR administrators and employees (via the ESS portal).
The Affordable Housing Levy (AHL) is a statutory deduction introduced under the Affordable Housing Act. It requires a 1.5% deduction from employee gross pay and an equal 1.5% employer matching contribution. BioTrack Payroll calculates and tracks both sides of the Housing Levy with a full audit trail, and includes it in all payslips and statutory reports.
Yes. BioTrack Payroll supports unlimited company entities under a single admin account. Each entity has completely isolated employee records, salary structures, statutory settings, and reports. This is ideal for group companies, holding structures, NGOs with multiple projects, and payroll bureaus managing multiple clients.
The ESS portal is a separate, secure login for employees to access their own payroll data without contacting HR. Employees can download monthly payslips in PDF, download their P9A annual tax certificate, view their year-to-date deductions, check leave balances, submit leave applications, and request personal detail updates. The ESS portal is completely isolated from admin functions.
Yes. BioTrack Payroll is used by NGOs, churches, manufacturers, and professional services firms across Kenya. NGOs and exempt organisations may have specific statutory configurations (for example, some are exempt from NITA). The system can be configured per your organisation's exemption status during onboarding.
Join 100+ Kenyan organisations running fully compliant payroll with BioTrack. Our implementation team handles the setup — you focus on running your business.
Local team · Nairobi, Kenya · Response within 24 hours