Payroll management in Kenya is rapidly evolving as businesses move away from spreadsheets and manual calculations toward smarter, cloud-based payroll software. With the Kenyan government enforcing stricter tax compliance and the demand for remote access to HR systems growing, cloud-based payroll solutions are no longer optional — they are essential.
This 2025 review breaks down the top 5 cloud-based payroll software solutions in Kenya that are transforming how companies manage salaries, statutory deductions, compliance, and employee records.
1. FaidiHR – Best Overall for Kenyan Businesses
FaidiHR is a homegrown payroll and HR automation platform built specifically for Kenyan companies. It provides a powerful yet user-friendly experience for managing payroll, HR, compliance, and employee self-service in one cloud-based platform.
Key Features:
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Automatic PAYE, NHIF, NSSF, and HELB deductions
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Bank-ready payroll files for salary disbursement
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Integrated KRA iTax support for PAYE filing
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Employee self-service portal (for payslips, leave, and more)
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Statutory reports: P9, P10, NHIF, NSSF
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Audit trail and role-based access control
Why Choose FaidiHR:
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Built for Kenyan law, regularly updated with tax changes
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Cloud-based: Access from anywhere, anytime
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Excellent customer support and onboarding
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Scalable from startups to enterprises
Pricing: Tiered based on company size, with packages for SMEs and customized plans for larger organizations.
Call: +254 702 339 699
Email: sales@faidihr.com
FaidiHR helps businesses focus on their core operations by automating manual HR and payroll processes.
2. Sage Business Cloud Payroll
A global provider with strong local adaptation, Sage is a popular choice among mid-sized and large organizations that need robust payroll and HR features.
Features:
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Multi-currency and multi-country support
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Leave management and reporting tools
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Scalable for organizations with complex structures
Best for: Enterprises with larger budgets and advanced payroll needs.
Considerations: Can be complex for smaller companies; higher pricing tiers.
3. QuickBooks Payroll (Kenya Edition)
QuickBooks is a globally known accounting tool that also offers payroll features customized for Kenyan businesses.
Features:
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Payroll runs and payslip generation
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Integration with QuickBooks Accounting
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Employee tax and benefit tracking
Best for: Companies already using QuickBooks for accounting.
Limitations: Some statutory compliance features may require manual setup.
4. Crystal HR Payroll (Cloud Version)
An established local provider, Crystal HR has moved its traditional desktop payroll system to the cloud, offering features that support Kenyan payroll laws.
Features:
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Statutory compliance: NHIF, NSSF, PAYE
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Leave and attendance tracking
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Employee record management
Best for: Manufacturing companies and the public sector.
Limitations: Interface may not be as modern or intuitive as newer solutions.
5. Zoho Payroll (Localized Integrations)
Zoho has begun offering payroll solutions adapted for different regions. With integrations and customizations, Kenyan businesses can use Zoho Payroll for cloud-based HR and finance management.
Features:
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Automated payroll processing
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Employee portals
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Integration with Zoho People & Zoho Books
Considerations: Requires configuration for full compliance with Kenya Revenue Authority (KRA) requirements.
Conclusion: Which One Should You Choose?
While each payroll system has its strengths, FaidiHR remains the top choice for Kenyan businesses in 2025 thanks to its:
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Full statutory compliance
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Simplicity and scalability
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Strong local support
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Affordable pricing
Whether you're a small business or a growing enterprise, switching to FaidiHR can save you time, reduce payroll errors, and help you stay compliant with all payroll laws in Kenya.
Ready to Automate Your Payroll?
Talk to a FaidiHR expert today.
Call: +254 702 339 699
Email: sales@faidihr.com
FaidiHR – Helping Kenyan businesses automate HR and payroll so they can focus on what matters.