Running payroll

Each pay period has one pay run. You prepare it as a draft, check it, and finalise it. Finalising locks the payslips, posts the run to Financials and adds it to the month's EMP201 and UIF declaration.

Preparing a run

1. Open Pay runs.
2. Click Prepare and the period, for example Prepare September 2026. If you have more than one pay cycle, the button starts with the cycle's name. If the run is already started, the button says Open instead.

The Dashboard also lists the run under What needs doing when it's time to prepare it.

The draft works out a payslip for everyone in the cycle who was employed in the period. At the top you see the run's Employees, Gross pay, PAYE and Net pay, with the total cost to the company.

Click Recalculate to work the draft out again, for example after changing an employee's details.

Changes since the last run

This list compares the draft with the last finalised run and shows what's different. Changes that need a look carry a Check badge and a tick box. Tick each one once you've checked it. You can't finalise the run until every flagged change is ticked.

If nothing changed, the list says Nothing to review and you can process the run in one step.

Not supported yet

If someone in the run has something Payroll can't calculate correctly yet, such as a pay item whose treatment isn't checked or pay below the minimum wage without an exemption, a Not supported yet card lists them with the reason and what to do. The run can't be finalised until the list is empty.

Once-off adjustments

For a bonus, overtime, unpaid leave or anything else that's only for this period:

1. In the Employees table, click Adjust next to the person. This opens their draft payslip.
2. Under Once-off adjustments, click Add a once-off adjustment.
3. Choose the Pay item. For an earning, choose whether it Adds to pay or Reduces pay.
4. Enter the Amount, or for hourly items the Hours, Rate per hour and Multiplier.
5. Optionally add text under Shown on the payslip, and click Add adjustment.

Payroll doesn't read leave from anywhere else. Enter paid and unpaid leave as once-off adjustments.

Hours from Track

For employees set to Pay from Track hours, the draft reads their hours from Track. A From Track section on the run shows the hours it used. Payroll can only read hours for an employee who is linked to their Looped account, the same link that gives them My pay.

If someone changes their hours in Track after the draft read them, the new figure shows next to the one in use and nothing changes until you click Use the new figures. Read again checks Track for changes. Finalising reads Track again first, and refuses the run if Track can't be reached and someone is paid from Track hours.

The payslip

Click an employee's name to see their payslip: Earnings, Deductions, Fringe benefits, Paid by the employer, the totals, and The full calculation showing each step of how their tax was worked out.

Finalising a run

At the bottom of the draft, the button is Process when there are no changes since the last run, and Finalise when there are.

1. Tick every flagged change.
2. If your company has A second person approves each run switched on, someone other than the person who prepared the run clicks Approve.
3. Click Finalise (or Process). The dialog shows the run's totals.
4. Confirm.

The payslips can't be changed afterwards, and the run is posted to Financials. See Payroll in the books for the journal it posts.

Finalising a run with changes needs the Finalise pay runs with changes permission. The Looped assistant can process a run with no changes, but only a person can finalise a run with changes.

After finalising

A finalised run links to its Bank payment file, the month's EMP201 and the month's UIF declaration.

Paying your employees

The Bank payment file lists each employee's net pay and account. Choose the format, Standard Bank (Business Online) or Any other bank (CSV), and click Download. Then import the file in your bank's online banking and release the payments there.

Accounts that changed since the last run, or that are being paid for the first time, are listed separately under Changed since the last run. Check them with each person before you release the batch: a changed bank account is the usual route for payroll fraud.

Downloading the file needs permission to see both bank details and salaries.

When the salary payments show on your bank statement, match them in Financials. See Paying salaries from the bank statement.

Sending payslips

Click Email payslips on the run to email every employee their payslip, at the email address on their record. Payroll tells you how many went and how many were skipped for having no email address. Nothing is emailed until you click it.

Employees linked to My pay see their payslip there as soon as the run is finalised, and get a Payslip ready notification if they've turned it on. See My pay.

Correcting a finalised payslip

A finalised payslip is never edited. You correct it on a later run instead:

1. Prepare the next run in the same tax year, if you haven't already.
2. Open the finalised payslip and click Correct this payslip under Corrections.
3. Under What happened, choose The payslip was wrong.
4. Choose the draft run to Pay it on, What was wrong (a pay item, or nothing for a UIF-only correction), the amount, whether UIF applied, and a Reason.

Payroll works the original month out again with the correction and pays the difference on the later run. The EMP201, UIF declaration and certificates count the correction in the original month. A correction on a draft run can be cancelled until that run is finalised.

Payroll can't correct across tax years, and it can't record an employee paying back pay they received (such as a commission clawback). Record those with your tax practitioner.

Reversing a run

Reversing undoes a finalised run and opens its period again so you can run it afresh. Use it for a mistake you catch before the month is filed.

1. Open the finalised run and click Reverse.
2. Say Why, for example "The bonus belonged in the next month".
3. Click Reverse run.

The run's journal in Financials is reversed. If the salaries were already paid, see When a run is reversed after it was paid.

Payroll refuses to reverse a run when:

• it isn't the cycle's latest finalised run;
• the month's EMP201 or UIF declaration is marked as submitted (correct the payslips on a later run instead, or undo "submitted" on the filing if it wasn't);
• someone in it was paid again later, in any cycle;
• one of its payslips has a correction on a later run;
• the next period's draft has once-off adjustments (remove them first);
• its tax year is closed.

Reversing needs the Reverse pay runs permission, and only a person can do it, never the assistant.

When someone leaves

1. Open the employee's page and, under Leaving, click End employment.
2. Enter their Last day and Why they left (the UI-19 reason code).
3. Enter any Leave owed (days). It's paid out in the last run at their daily rate.
4. Check Notice pay. Payroll fills it in from the BCEA and their length of service; change it if their contract says more, or clear it if they work their notice.
5. Save.

Their last run pays them to their last day, with the leave owed and notice pay. Once that run is finalised, you can preview or download their UI-19 from the same card, to sign and give them for their UIF claim. Take back undoes the ending if you recorded it by mistake.

Ending someone's employment needs permission to change pay; the UI-19 needs permission to see salaries and ID numbers.