Multi-branch payroll in Kenya without losing your mind
Running staff across 3 branches with NHIF/SHA + NSSF + PAYE used to mean a Saturday at your desk. Here's how the multi-branch payroll module compresses it to ten minutes.
If you're running a small chain — three pharmacies, four mini-marts, two salons — payroll month is the part of the month nobody enjoys. Each branch tracks its own staff, attendance lives in someone's WhatsApp group, NHIF/SHA forms have to be reformatted, and the bank file has to be assembled from spreadsheets.
We built multi-branch payroll for the customer who finally lost a Saturday to it and threatened to quit. Here's the workflow, step by step.
Setup, once. Add each branch and assign staff to them. Set commission and overtime rules per role. Configure your statutory rates (NSSF tier I and II, NHIF/SHA per band, PAYE). Configure your bank for direct debit (Equity, KCB, Co-op all work).
Monthly, ten minutes. Open Payroll → Run for May. Omnix pre-fills attendance from the time-clock module (or you import a CSV). Adjust the few rows that need fixing — overtime exceptions, mid-month joiners, leave settlement. Click Calculate. Review the variance against last month. Click Approve.
The output is three files: a bank batch CSV ready to upload to your business banking portal, a NHIF/SHA-formatted XML, and an NSSF Tier I + II batch. P9, P10 and PAYE filings are generated for the next month's iTax submission.
What you don't have to do anymore. Reformat statutory forms. Manually calculate per-branch commission splits. Re-key bank batches. Cross-check that the Saturday and Sunday hours got the right multiplier.
Honest caveat. First-time setup takes about 2 hours per branch — you have to enter staff, contracts, and statutory bands. That's a one-time cost. After that, every month is ten minutes.
The module is included in the Business tier (KES 75,000 one-time). If you have the Starter tier and want it, add the Business upgrade for KES 45,000 (the difference).