HRMS Software for Businesses in Kenya

Nathan HRMS is HRMS software for Kenyan businesses that need one system for employee records, recruitment, attendance, leave, payroll, approvals and workforce reporting.

Nathan HRMS connects information across HR, payroll, finance and operations so that each function works with the same employee records. For Kenyan payroll, the platform can be configured around the earnings, deductions and reports your organisation needs.

This guide explains what Nathan HRMS includes, how its capabilities support Kenyan operations and what implementation can involve.

Keep Employee Information and HR Processes Connected

Nathan HRMS provides a central employee record covering recruitment, onboarding, employment changes and departure.

Recruitment teams can publish vacancies, manage applications and track candidates through defined hiring stages. AI-assisted candidate screening helps organise initial application reviews, while hiring managers can record interview feedback and decisions within the platform.

Once a candidate is hired, their information can move into the employee record without creating another profile manually. HR can then manage personal details, employment information, reporting lines, documents, approvals and organisational data through the same system.

The platform supports:

• Recruitment and applicant tracking

• Candidate-to-employee conversion

• Onboarding and offboarding

• Internal transfers

• Employee reboarding

• Departments, branches and reporting structures

• Company policies and documents

• Multiple companies and legal entities

For organisations operating across several branches, sites or legal entities, this provides a shared workforce structure while preserving the access controls required by each business unit.

Connect Attendance and Leave Directly to Payroll

When attendance, leave and payroll operate through separate processes, payroll teams need to collect, reconcile and check information before every pay run.

Nathan HRMS connects approved attendance, leave, overtime, commissions and other payroll inputs with the employee record. Employees can record attendance through supported biometric devices, mobile check-ins or GPS-based check-ins, depending on your configuration.

You can configure:

• Work schedules and rosters

• Attendance rules

• Leave types and balances

• Overtime policies

• Approval routes

• Attendance exceptions

• Manager permissions

Managers can review exceptions and approve employee requests within the platform. Once approved, the information is available for payroll without maintaining a second attendance record.

This gives HR, payroll and operations a shared process for managing employee time while preserving an approval trail for review.

Manage Kenyan Payroll Information and Deductions

Nathan HRMS can bring together the employee information, earnings and deductions used during payroll processing.

Payroll records can include:

• Basic salary

• Approved attendance and overtime

• Leave inputs

• Allowances and deductions

• Commissions and incentives

• Employee payslips

• Payroll summaries

• Finance reports

For Kenyan employers, the payroll configuration also needs to account for statutory requirements such as Pay As You Earn (PAYE), National Social Security Fund (NSSF) contributions, Social Health Insurance Fund (SHIF) contributions and the Affordable Housing Levy (AHL).

Authorised users can review payroll information before approval. Employees can then access their payslips through the employee portal or mobile app.

The exact calculations, statutory reports and automated outputs available for your Kenyan payroll requirements should be confirmed during configuration.

Prepare Payroll Data for Kenyan Statutory Processes

Accurate payroll records support the tax returns, contributions and payments managed through Kenyan government portals.

The Kenya Revenue Authority’s PAYE guidance explains that employers must deduct PAYE from employment income and remit it to KRA. It also identifies SHIF contributions and the Affordable Housing Levy as deductions used when determining taxable employment income.

Payroll data can support processes involving:

• PAYE calculations and returns

• NSSF contribution records

• SHIF contribution records

• Affordable Housing Levy calculations

• Employee payslips

• Payroll summaries

• Finance reports

• Payroll audit records

NSSF contribution rates are updated according to the statutory implementation schedule. The NSSF notice to employers confirms the applicable Year 4 contribution rates for 2026.

Employers manage SHIF contributions through the Social Health Authority’s employer process. The SHA Employer Portal terms state that employers are responsible for accurate and timely employee contributions.

Keeping salary, deduction and employee information within one payroll process helps your team review figures before completing returns and payments. Final submissions remain the responsibility of your organisation and authorised payroll or tax representatives.

Give Employees Access Without Losing HR Control

Employee self-service reduces routine HR administration while keeping access governed by role and permission.

Through the Nathan HRMS web portal or mobile app, employees can:

• Review payslips

• Submit leave requests

• Check leave balances

• Upload documents

• Update permitted personal information

• Record attendance through configured methods

Managers can review team attendance, respond to requests and complete approvals without relying on email threads or manually maintained trackers.

Notifications can also connect with Microsoft Teams, Slack, WhatsApp and email, depending on the integrations selected.

Manage Performance and Employee Development

Nathan HRMS links performance management to the employee’s role, department and reporting structure.

Managers can define goals and key performance indicators (KPIs), complete performance reviews, collect 360-degree feedback and create development plans. Authorised teams can also use calibration tools to review performance outcomes across departments or employee groups.

Learning and development activity can be recorded alongside performance information. This gives HR and management a consolidated view of employee goals, feedback, development activity and review history.

Give Management Better Workforce Visibility

Nathan HRMS provides dashboards and reports covering areas such as:

• Headcount

• Attendance and absence

• Leave

• Payroll

• Recruitment

• Employee turnover

• Performance

• Workforce costs

Access can be configured by role so that HR, finance, payroll and management teams see information connected to their responsibilities.

AI-assisted reporting tools allow authorised users to ask workforce questions and generate summaries using information available in the platform. This supports management reporting without distributing multiple versions of employee and payroll spreadsheets.

Connect HRMS Data With Your Existing Systems

Nathan HRMS provides more than 35 prebuilt integrations and an open application programming interface.

Supported integration categories include:

• ERP and finance systems

• Identity and access-management platforms

• Biometric attendance devices

• Banking and payroll processes

• Microsoft Teams, Slack, WhatsApp and email

• Custom systems through REST APIs and webhooks

Integration planning should establish which system owns each data field, how information moves between platforms and who reviews unsuccessful transfers.

This helps prevent duplicate employee records and conflicting information across HR, finance and operational systems.

Apply Permissions, Security Controls and Audit Records

Nathan HRMS contains identity information, bank details, salary records, employment history and other personal information. Access therefore needs to reflect each user’s responsibilities.

The platform provides role-based permissions, authentication controls, encrypted data storage and activity logging. Its security framework also covers backups, infrastructure monitoring, database separation and controlled access to stored files.

Audit records allow authorised teams to review system changes, approvals and user activity. Permissions can be configured for employees, managers, HR administrators, payroll teams and other approved roles.

These controls should form part of your organisation’s data governance and retention processes under Kenya’s Data Protection Act, 2019.

Configure Nathan HRMS Around Your Organisation

Nathan HRMS can be configured around your entities, branches, departments, reporting lines, approval routes, attendance policies and payroll requirements.

Implementation can include:

1. Reviewing your HR and payroll processes

2. Configuring companies, branches and reporting lines

3. Setting attendance, leave and approval rules

4. Preparing and validating employee data

5. Configuring earnings and deductions

6. Setting up payroll reports

7. Connecting approved integrations

8. Testing workflows and calculations

9. Training administrators, managers and employees

10. Launching the platform in agreed stages

Historical employee and payroll information should be validated during migration. Parallel testing can help your team check payroll results before the system becomes the primary payroll environment.

The implementation scope will depend on your workforce size, entities, payroll structure, data quality and integration requirements.

Nathan HRMS Capabilities for Kenyan Businesses

Bring Your Kenyan Workforce Operations Into One System

Nathan HRMS gives Kenyan businesses one platform for managing employee records, recruitment, attendance, leave, payroll information, performance and workforce reporting.

For HR and payroll teams, this reduces repeated administration and provides a structured approval record. Finance and management gain access to reliable workforce and payroll information, while employees can manage routine requests without removing HR oversight.