Running payroll in Kenya isn’t just about paying employees—it’s about staying compliant, reducing errors, and improving operational efficiency. With the growing demand for automation and evolving regulations from bodies like KRA, NHIF, and NSSF, more businesses are turning to modern payroll systems to streamline operations.
But how do you choose the right payroll system for your business?
This guide helps you evaluate what to look for and why FaidiHR is a top choice for businesses in Kenya.
Why Choosing the Right Payroll System Matters
The payroll system you select can impact:
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Your compliance with tax and labor laws
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Accuracy of salary and deduction calculations
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Your employees’ trust and satisfaction
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Efficiency in HR and finance operations
A poor choice can result in costly errors, penalties, or delays. A good system simplifies tasks and empowers your team.
Key Factors to Consider When Choosing a Payroll System
1. Local Compliance
Ensure the system automatically calculates:
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PAYE (Pay As You Earn) and integrates with KRA iTax
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SHIF, NSSF, and HELB deductions
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Generates statutory returns like P9, P10, and remittance reports
A locally compliant system keeps your business aligned with Kenyan tax laws and reduces the risk of penalties.
2. Cloud-Based Access
Cloud-based payroll systems allow you to:
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Access data remotely
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Secure backups automatically
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Enable real-time collaboration across departments
This is especially useful for businesses with distributed teams or hybrid work arrangements.
3. Ease of Use
Choose a system with a clean, intuitive interface. Your HR or finance staff should be able to:
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Onboard new employees easily
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Run payroll in a few clicks
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Generate payslips without technical training
4. Employee Self-Service Portal
A good system should include a self-service portal where employees can:
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Download their payslips
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Apply for leave
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View attendance records
This reduces administrative work and improves transparency.
5. Scalable and Affordable Pricing
Whether you’re a small business or scaling fast, the payroll system should:
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Offer affordable packages
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Allow upgrades as your employee count grows
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Avoid hidden charges or expensive customizations
Why FaidiHR is the Right Payroll System for Kenyan Businesses
FaidiHR is a cloud-based HR and payroll solution designed specifically for Kenyan businesses. It combines automation, compliance, and ease of use in a single platform trusted by SMEs and larger organizations alike.
Key Features of FaidiHR:
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Auto-calculates PAYE, SHIF, NSSF, and HELB
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KRA iTax integration
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Statutory report generation (P9, P10, SHIF, NSSF)
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Employee self-service portal
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Bank-ready salary files
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Leave and attendance tracking
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Audit trail and role-based access
Affordable Pricing:
FaidiHR offers flexible pricing that fits the budget of growing businesses, with options to scale as your team grows.
Final Thought
The best payroll system is one that fits your business size, complies with local laws, and is easy to use. Investing in the right system will not only save you time and money—it will also enhance accuracy, compliance, and employee satisfaction.
FaidiHR delivers all that and more, making it one of the most reliable payroll systems for businesses in Kenya today.
Talk to Us
Start automating your payroll the smart way.
Call: +254 702 339 699
Email: sales@faidihr.com
FaidiHR – Helping Businesses Focus by Automating Manual HR and Payroll Processes.