Kenyan Payroll Software

Fully Compliant
Kenyan Payroll
Software

Automate PAYE, NSSF, SHA, NITA, and Housing Levy with a secure, multi-company payroll system built for Kenyan businesses, churches, and enterprises.

PAYE Auto Calculation
NSSF & SHA Compliance
Multi-Company Support
Employee Self Service (ESS)
BioTrack Payroll — Admin Live
January 2026 Payslip
Sarah Wanjiku
Net Pay
KES 61,563
Gross Pay85,000.00
PAYE– 15,503.45
NSSF (Tier I + II)– 4,320.00
SHIF– 2,338.00
Housing Levy– 1,275.00
Net Pay61,563.55
Compliance — Jan 2026
PAYE NSSF SHIF NITA Housing Levy P9A
Multi-Company View
Company A
Company B
Company C
Employees
45
Status
✓ Active
Last Payroll
Jan 2026
NSSF Tier
I + II
KRA Compliant PAYE NSSF Tier I & II SHIF (SHA) NITA Housing Levy P9A / P10A iTax Export
Platform Features

Everything You Need to Run Payroll With Confidence

Purpose-built for Kenyan statutory compliance — from PAYE to Housing Levy, calculated accurately every month, across every company.

🏛️

Statutory Compliance

All Kenyan statutory deductions computed automatically and updated in line with KRA and regulatory changes — no manual intervention required.

  • PAYE — computed against KRA tax bands with personal relief
  • NSSF Tier I & Tier II — employer and employee contributions
  • SHIF — SHA-compliant rates replacing NHIF from Oct 2024
  • NITA — National Industrial Training Authority levy
  • Housing Levy — 1.5% employee + 1.5% employer tracking
  • P9A & P10A — KRA-ready annual tax certificates
🏢

Multi-Company Payroll

Run payroll for multiple entities, subsidiaries, or client companies from a single admin account — with full data isolation per company.

  • Unlimited companies under one subscription
  • Separate employee records and statutory settings per entity
  • Centralized admin with role-based access control
  • Consolidated management reporting across all entities
  • Per-company payslip branding and bank file generation
  • Switch between companies in a single click
👤

Employee Self Service (ESS)

Give employees a secure, dedicated portal to access their own payroll data — reducing HR overhead significantly.

  • Monthly payslip download in PDF format
  • Annual P9A tax certificate for KRA compliance filing
  • Year-to-date deductions and tax summary
  • Leave balance view and application submission
  • Personal detail update requests routed to HR
  • Separate secure login — fully isolated from admin
📊

Reports & Exports

Every statutory report and submission file needed for compliance — formatted exactly as required by each Kenyan authority.

  • iTax-ready PAYE return files for KRA submission
  • NSSF contribution schedules (CSV upload format)
  • SHIF / SHA deduction reports and schedules
  • NITA levy export per employee
  • Housing Levy schedules with employer matching
  • Bank transfer files — multiple formats supported
How It Works

Process Payroll in Four Steps

A repeatable, audit-ready workflow — from employee setup to statutory submission.

1 👥

Add Employees

Import employee records via CSV or add manually. Set salary structures, KRA PIN, tax relief, and statutory settings per employee.

2 ⚙️

Process Payroll

Run payroll for the month in one click. PAYE, NSSF, SHIF, NITA, and Housing Levy are all calculated and verified automatically.

3 📄

Generate Reports

Produce payslips, P9A, P10A, and bank payment files. Review and approve before any payment or submission is made.

4

Submit Returns

Export iTax-ready files and statutory schedules. Submit PAYE to KRA and contribution files to NSSF, SHA, and NITA directly.

Statutory Compliance

Every Deduction.
Every Month.
Every Time.

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.

P
PAYE — Pay As You Earn
KRA tax bands with personal relief, insurance relief, and mortgage relief applied per employee.
N
NSSF — Tier I & Tier II
Employee and employer contributions per the NSSF Act 2013. Contribution schedules generated for upload.
S
SHIF — Social Health Insurance
SHA-compliant rates replacing NHIF. Updated automatically from October 2024 transition.
N
NITA — Training Levy
National Industrial Training Authority levy calculated and exported per employee per month.
H
Housing Levy (AHL)
1.5% employee deduction + 1.5% employer matching. Both sides tracked with full audit trail.
Live Calculation — KES 85,000 Gross · January 2026
Gross Pay85,000.00
PAYE Tax– 15,503.45
NSSF Tier I– 480.00
NSSF Tier II– 3,840.00
SHIF Contribution– 2,338.00
Housing Levy– 1,275.00
Total Deductions– 23,436.45
Net PayKES 61,563.55
PAYE NSSF SHIF NITA Housing Levy KRA Compliant
Employee Portal Self Service
👤
Sarah Wanjiku
Senior Accountant · Company A
📄
Download Payslip
📋
P9A Certificate
🏖️
Leave Balance
✏️
Update Details
Recent Payslips
January 2026KES 61,563PDF ↓
December 2025KES 61,563PDF ↓
November 2025KES 61,563PDF ↓
Employee Self Service

A Secure Portal for Every Employee

Reduce HR overhead by giving employees direct access to their own payroll records. Completely separate login, completely separate session — isolated from all admin functions.

📄
Payslip Downloads
Access and download monthly payslips in PDF format at any time.
📋
Annual P9A Tax Certificate
Year-end P9A certificate for KRA compliance filing and tax returns.
📊
YTD Tax Summary
Year-to-date tax and deduction breakdown for personal financial planning.
🏖️
Leave Management
View leave balances and submit leave applications directly through the portal.
✏️
Personal Detail Updates
Request updates to personal information — routed to HR for approval.
Track Record

Trusted by Kenyan Organisations

From churches and NGOs to manufacturers and multi-company groups across Kenya.

100+
Organisations running payroll
99.9%
Platform uptime SLA
256-bit
SSL encrypted data storage
100%
KRA compliance accuracy
★ ★ ★ ★ ★

"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."

💼
Sarah Wanjiku
HR Manager · TechStart Kenya Ltd
★ ★ ★ ★ ★

"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."

🏢
James Kariuki
Group Finance Director · Kariuki Holdings
★ ★ ★ ★ ★

"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."

👩‍💼
Grace Muthoni
Head of People · Muthoni Enterprises
Pricing Plans

Structured for Every Organisation Size

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.

Starter
SME & Small Teams
Up to 50 employees · Single company
Custom Pricing
Contact sales for your quote
Request Demo
  • Up to 50 employees
  • Single company payroll
  • Full statutory compliance
  • Monthly payslip generation
  • P9A & P10A reports
  • iTax export files
  • Email support
Recommended
Growth
50–500 employees · Multi-company
Custom Pricing
Based on headcount & entities
Book Consultation
  • Everything in Starter
  • Multi-company payroll
  • Employee Self Service (ESS) portal
  • Advanced reports & analytics
  • Bank payment file generation
  • Role-based admin access
  • Priority support
Enterprise
Large Organisation
500+ employees · Unlimited entities
Tailored Pricing
Structured to your operations
Talk to Sales
  • Everything in Growth
  • Unlimited employees & companies
  • Dedicated account manager
  • SLA-backed uptime guarantee
  • Custom integrations
  • On-premise deployment option
  • Dedicated onboarding team
⚠ One-Time Setup & Onboarding Fee Applies — includes data migration, employee import, statutory configuration, and a dedicated implementation session.
Get Started

Ready to Automate
Your Payroll?

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

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