Paying staff a year-end bonus through payroll
How a shop pays a year-end or festive bonus on its regular pay run, with the tax, the second approver, the payslips and the cash planned in advance.
By Achekam · · 5 min read · For Retail businesses in South Africa, Nigeria, Kenya
December is the month retail staff earn their keep. Trading hours stretch, the stockroom never empties, and the tills run from opening to close. Many shop owners want to say thank you with a festive or year-end bonus, and staff often count on it.
The payroll question is practical. Achekam has no separate bonus run, so the bonus has to travel on the regular pay run with everything else. Done carelessly, that means a rushed decision on the last Friday, a pay run nobody is allowed to approve, and a bank balance that cannot cover the extra tax. Done with a little planning, it is one of the easier things payroll does all year.
Deciding the bonus and who qualifies, in writing
Settle the rules before anyone touches payroll. Write down:
- Who qualifies. Permanent staff only, or casuals who worked the season as well? Staff who resigned in November? A cashier who started in October?
- How it is worked out. A fixed amount per person, a share of a month's pay, or an amount tied to a store target such as shrinkage or sales.
- Whether it is promised or discretionary. If employment contracts promise a thirteenth cheque, it is not a gift you can skip in a bad year. Read the contracts.
- When it is paid. With the December pay or earlier, so staff have it before the festive weekend.
Have the owner or managing director sign the list of names and amounts. That signed list is what payroll works from and what an auditor will ask for later.
Adding it as a variable input on the regular run
Pay runs in Achekam can be monthly, fortnightly or weekly, and each period's overtime, commission, allowances, reimbursements and unpaid leave go in as variable inputs. There is no separate bonus, correction or final-settlement run: a bonus goes in as a variable input on the regular run for the period in which you pay it.
For a shop with a weekly run for floor staff and a monthly run for managers, that means choosing which period's run carries each person's bonus. Enter each amount against the right employee from the signed list, and have a second person tick each one back to the list before the run moves on. Typing errors in a bonus month are expensive because the amounts are larger than usual.
Tax in the bonus month, worked out from the confirmed table
A bonus is taxable pay, so the tax deducted in the bonus period will be higher than in an ordinary period. Warn staff in advance, or the first questions you get will be about why the net amount is smaller than they expected.
The calculation comes from a tax table that a named person has confirmed:
- South Africa. PAYE, UIF and SDL come from a table stored as data, and a run is refused until that year's table is confirmed. The calculation applies the tax brackets, age rebates, medical tax credits and retirement-contribution limit, caps UIF at the ceiling and applies the SDL exemption. Only the 2025/26 table ships, so for pay dates from 1 March 2026 you must start the 2026/27 table from last year's figures, update it to SARS's figures and confirm it. Do that well before December. SARS sets out how employers must deduct PAYE, with the year's tables and rebates, in its Guide for Employers in respect of Employees' Tax.
- Nigeria. PAYE is worked out on the Nigeria Tax Act 2025 bands, with pension, the opt-in National Housing Fund, NSITF, the ITF levy, rent relief and the minimum-wage exemption, from a table a person confirms.
- Kenya. PAYE is worked out with personal and insurance relief, NSSF Tier I and II, SHIF, the Affordable Housing Levy and the NITA levy.
For Nigerian and Kenyan employers, only the 2026 tables ship and the app can confirm a table but not create one, so a bonus paid in December 2026 sits inside a year the app already covers. Check that the table is confirmed before you load the bonus inputs.
Approval by someone who is not paid on the run
Every pay run is approved by someone other than the person who prepared it, nobody can approve a run that pays themselves, and an approved run is never recalculated. In a small shop that rule bites in the bonus month. If the owner draws a salary through payroll, and the store manager prepares the run, who approves it?
Sort it out in November:
| Person | Can approve this run? | Why |
|---|---|---|
| The bookkeeper who prepared it | No | The preparer never approves |
| A store manager paid on it | No | Nobody approves a run that pays them |
| The owner, paid on the managers' run only | Yes, for the weekly floor-staff run | That run does not pay the owner |
| A second payroll user who neither prepared it nor is paid on it | Yes | Both conditions are met |
Because an approved run is never recalculated, check everything before approval: the bonus inputs, the tax, the net pay. A mistake found afterwards has to be fixed on a later run as a variable input, not by reopening the bonus run.
Payslips that show the bonus
Payslips are PDFs carrying your logo and business details, downloadable or e-mailed one per person. An employer setting sends them automatically when a run is approved, with a delivery log showing what went out. E-mailing needs an e-mail service configured on the server.
Before approving, open a sample payslip for someone receiving a bonus and look at it as the cashier will. Is the bonus visible, and is the higher tax easy to follow? Staff read December payslips closely. A clear payslip saves a queue at the office in January.
The wages journal and the cash the run needs
An approved pay run is posted to your own ledger as a wages journal, with the amounts owed to the tax authority and the funds recorded as liabilities. The bonus therefore lands in the same month's wage cost, and the extra tax lands in the liabilities you pay over afterwards.
Achekam moves no money. Each approved run has a payment schedule you can download as CSV, and marking it paid only records the fact. South African employers can also produce a wages file for the bank in FNB's import layout or a column-mapped CSV for Standard Bank, Absa, Nedbank or another bank.
Plan the cash in two parts: the net pay going to staff, and the larger tax and fund payments due the following month. In retail, December takings help with the first; January, when trade slows, has to cover the second.
For other pay that changes from period to period, see paying instructors per class and weekly payroll for casual staff. If some staff owe you money from earlier in the year, salary advances and staff loans explains how recoveries run alongside a bonus.
Before the festive rush
In early November, confirm the year's tax table, agree who approves the December runs, and get the signed bonus list. Then the bonus month becomes an ordinary pay run with larger numbers, rather than a scramble on the busiest trading weekend of the year.
General guidance only, not advice on your own circumstances. Tax and payroll rules change: check the current position with the authority or your adviser.
