FINANCE & ACCOUNTING · SERVICE 11

Payroll Outsourcing in Kenya

Endpoint Logic processes monthly payroll for Kenyan businesses of all sizes — computing gross pay, deductions (PAYE, NHIF, NSSF), and net pay, issuing payslips, and filing statutory returns on time with KRA iTax, the NHIF portal, and NSSF. Payroll runs on your schedule and is ready for your bank payment before your cutoff date.

Last updated 22 October 2026

What's included

  • Monthly payroll computation Gross pay, allowances, PAYE, NHIF (SHA), NSSF, HELB, and any other deductions computed accurately for each employee.
  • Payslip generation Payslips issued to employees by email or a self-service portal, formatted clearly with all deductions itemised.
  • Bank payment file Payment file or schedule prepared and sent to you for approval before your bank transfer deadline.
  • PAYE returns (P10) Monthly PAYE return filed on KRA iTax before the 9th of the following month.
  • NHIF and NSSF remittances Deduction schedules prepared and payments made to NHIF (SHA) and NSSF portals on your behalf.
  • Year-end P9As P9A certificates prepared for each employee at year-end for their personal tax returns.

How engagement works

#StepTypical timing
01 SetupEmployee details, payroll structure, allowances, and deduction rules entered and verified. 3–5 days
02 Monthly inputYou provide any changes (new hires, leavers, salary changes, overtime) by your agreed cutoff date. By agreed cutoff
03 Processing and reviewPayroll computed. Summary sent for your review and approval before payslips are issued or payments made. 1–2 days
04 Filings and remittancesPAYE, NHIF, and NSSF filed and remitted by statutory deadlines after your payment approval. By 9th of following month

Technologies and tools

We work with the tools you already run where possible. Common technologies we support:

  • KRA iTax
  • NHIF (SHA) portal
  • NSSF portal
  • HELB portal
  • QuickBooks Payroll
  • Sage Payroll
  • BrightPay
  • Excel

Frequently asked questions

When do I need to send payroll inputs?

We agree a cutoff date with you — typically 3–5 working days before your payment date. You send changes (new hires, leavers, adjustments) by that date, and we have payroll ready for your review and approval before the bank transfer deadline.

Do you file PAYE on our behalf?

Yes. We file the monthly P10 return on KRA iTax and can make the payment on your behalf using your KRA credentials, or prepare the payment details for you to make directly.

What happens when there are statutory changes?

We monitor KRA, NHIF, and NSSF for changes to rates and regulations and apply them automatically before they take effect. You are notified of any changes that affect your payroll.

How are payslips sent to employees?

By default we send password-protected payslips directly to each employee's email address. We can also integrate with a self-service payroll portal if you prefer.

Is payroll information kept confidential?

Salary information is handled with strict confidentiality. Access is limited to the team members processing your payroll, and all data is held securely.