Collecting variable pay inputs from clients

How a payroll bureau collects overtime, commission, allowances and unpaid leave from clients before each run, using standing requests and cut-offs.

By Achekam · 11 October 2026 · 5 min read · For Accountants & audit firms in South Africa, Nigeria, Kenya

The fixed part of a payroll looks after itself. Salaries, standing allowances and regular deductions are set up once and repeat every period. The trouble is everything else: the overtime a supervisor approved on a scrap of paper, the sales commission that depends on a report finance has not finished, the employee who took three unpaid days and the travel claim that arrived by WhatsApp.

These variable inputs are where most payroll errors start, and in a bureau they arrive from outside, in whatever form the client finds convenient. The bureau's job is to turn that stream into one complete, dated, approved set of inputs for each run. This article sets out a way to do it.

Inputs that change every period

In Achekam, pay runs can be monthly, fortnightly or weekly, and each period's overtime, commission, allowances, reimbursements and unpaid leave are entered as variable inputs on that run. Everything that is not part of an employee's standing pay belongs in this category.

Ask each client, at onboarding, to list the variable items it actually uses, and for each one: who at the client approves it, how it is calculated, and what evidence exists. A builder's list will be dominated by overtime and site allowances; a car dealership's by commission. Knowing the list in advance means the bureau can spot a missing item instead of waiting for a complaint.

Allowances deserve particular care, because their tax treatment varies. For South African clients, SARS's Guide for Employers in respect of Allowances explains how subsistence, travel and other allowances are treated for PAYE, with the legal references and worked examples. Settle the treatment of each allowance with the client once, in writing, rather than deciding it period by period.

A standing request to the client

The most reliable way to collect inputs is to ask for them the same way every period. Achekam's RFI console lets staff create, send and track requests to clients for documents, answers and confirmations in one place. A request made for payroll inputs works like any other:

• The client opens it from a personal e-mailed link, without an Achekam account. The firm can also require a one-time code sent to the client's e-mail.
• Staff accept or reject each item the client sends, and can return the request saying what is still missing.
• Automatic reminders go every 3 days by default, up to 5 per request, and can be switched off.
• Reusable request templates live under RFI Templates, so a payroll inputs request can be set up once and reused.

For a monthly client, build one template listing the items: approved overtime, commission schedule, new allowances, reimbursement claims, unpaid leave, starters and leavers. Send it on the same day each period. The client learns the rhythm, and the request history shows exactly when inputs were asked for and when they arrived.

Cut-off dates the client agrees to

A request without a deadline is a suggestion. Agree a cut-off with each client, set early enough for the bureau to calculate, review and approve the run before payday, and put it in the engagement letter.

Then agree what happens after the cut-off. The cleanest rule is that anything received late goes into the next run, unless the client's named contact asks for an exception in writing and accepts that payday may move. A bureau that quietly accepts late inputs every month trains its clients to send them late.

Make the cut-off visible: in the request itself, in the calendar of whoever prepares the run, and in the reminder text the client receives.

Frozen once the run is approved

Each run can be recalculated as often as needed until it is approved. Once it is approved, its variable inputs are frozen. Nothing is added to an approved run.

That freeze is a feature. It means the figures behind a payslip cannot shift after the payslip has gone out. It also means the bureau needs a routine for what arrives too late:

1. Log the late input with the date it arrived.
2. Tell the client it will be paid in the next run, and why.
3. Capture it on the next run with a note referring to the original period.
4. Ask the approver of that run to check it specifically.

Unpaid leave needs a decision rather than an automatic entry. Unpaid leave does not cut pay automatically: payroll is warned and decides. The bureau should confirm with the client, every time, that the days were genuinely unpaid before reducing anyone's pay. Leave records more generally are covered in keeping leave balances for clients' staff.

Bonuses and final pay are inputs too

There is no separate bonus, correction or final-settlement pay run. A bonus, a correction to an earlier period or an employee's final pay goes in as variable inputs on the regular run.

Plan for that in the request template. Add a line asking whether any bonus, back pay or leaver is due this period, so the client has to answer it each time. Then check what the calculator can handle. On South African payroll, each run works out gross pay, PAYE, UIF and SDL per employee, but the calculator does not handle lump sums without a directive, backdated pay or retrenchment packages, and returns warnings instead. SARS tax directives (IRP3) can be recorded and applied. When the client's answer is yes to any of these, the preparer should read every warning on the run before passing it to the approver.

A summary of who does what:

The full month for a South African client, from inputs to filing, is laid out in a South African bureau's monthly payroll cycle.

Build the inputs request template for your largest client this week, agree its cut-off in writing, and send it for the next run. Use what you learn to set up the rest.

General guidance only, not advice on your own circumstances. Tax and payroll rules change: check the current position with the authority or your adviser.