Run a Pay Run

A pay run pays one pay cycle for one pay period. Microkeeper works out each employee's payslip from their approved timesheets, leave and pay rules. You check and adjust the payslips, then complete the pay run: pay your team from the ABA file and lock it, so staff see their payslips.

Navigate to Menu > Payroll > Payruns.

Before you start a pay run

• Timesheets are approved. With Tick Approval, only approved shifts are paid. See Timesheets.
• Leave requests in the period are reviewed. Only approved leave is paid. See Reviewing Leave.
• Each employee has a start date and pay cycle on their profile. Staff whose start date is after the pay period aren't included.

Start a pay run

1. On the Upcoming Payruns tab, click Start next to the pay cycle. The New Payrun window shows the next pay period to pay.
2. Check the Year and Run, the pay period's dates. To pay an earlier period, choose its financial year under Year, then its Run.
3. Check the Payment Date, the day staff are paid. Choosing a Run fills it in from the period's end date and the pay cycle's payment days in arrears.
4. Read the messages under Payment Date, such as pending leave requests in the period. Click Leave Request to review one.
5. Click Payrun. Microkeeper works out the payslips, and the pay run shows on the Processed tab.

When you pay earlier periods, pay them oldest first, so leave balances and year-to-date totals carry forward. A message that the next run is expected to be a later one can be ignored when you're paying an earlier period on purpose.

Birthdays lists staff with a birthday in the period, whose junior rate may change. For the first pay run of a financial year, check Runs in year: the number of pay runs expected in the year, such as 52 or 53 for weekly.

Review the payslips

On the Processed tab, click View next to the pay run. The Summary tab totals the pay run, and the Payslips tab shows each employee's payslip:

• Payments: each line of pay, with its Class, STP Category, rate, hours and multiplier, and super.
• The employee's leave balances and the hours paid.
• Expenses: amounts taken before tax, such as salary sacrifice.
• Deductions: amounts taken after tax, such as union fees.
• Tax and Net Earnings.

The buttons above each payslip:

Change a payslip

• To add a line, click + in the Payments, Expenses or Deductions heading.
• To change or delete a line, click its pencil.

For a payment, enter the Title shown on the payslip, the Rate, Hours and Multiplier, and choose its Class and STP category. Click Add Payment. The Class decides whether it attracts super and builds up leave. See the Payments Classification Chart.

Lines you add stay on the payslip when it's reprocessed. If you make the same change every pay run, add a pay rule instead. See How Pay Is Calculated.

Make the same change for many staff

Click Bulk Actions, then Payment, Leave, Expense or Deduction.

1. Tick the staff it's for.
2. Enter each one's Title, Rate, Hours, Multiplier, Classification and STP.
3. Click Add Payments.

To add them from a spreadsheet, click Template / Export for the file's columns: Employee, Title, Rate, Hours, Multiplier, Classification, STP and Tax Method, plus Date, Location, Role and Job if you track them. Click Import Payments via CSV, check the lines it fills in, and click Add Payments.

Reprocess a pay run after changes

If you change a timesheet, a profile, a setting or a pay rule after starting the pay run, reprocess so the payslips use it:

• For one employee, click Reprocess above their payslip, then Confirm Reprocess.
• For everyone, click Bulk Actions, then Reprocess. Tick I understand and click Confirm Reprocess Payrun.

Reprocessing works out the lines again, and keeps the lines you added. It only covers staff already in the pay run: to add someone, click Bulk Actions, then Add Employee.

Pay an employee's final pay

1. Click Final above the employee's payslip.
2. Check the leave to pay out, such as Annual Leave hours and Leave Loading, and any other balances.
3. Check the Termination Date, and choose the Cessation Type, such as Voluntary or Redundancy.
4. Click Terminate.

The employee is made inactive, their leave is paid out on the payslip, and the payslip is marked as final for Single Touch Payroll.

Complete the pay run and pay your team

Click Complete Payrun. Under 1. Pay Your Team:

1. Confirm Payment Date: check the date staff are paid.
2. Create a backup: click Download Backup to keep a copy of the payslips.
3. Download the ABA file: click Download ABA. It pays each employee's Net Earnings into their bank account.
4. Upload the ABA file to your bank through your online banking.
5. Lock the Payrun: click Lock & Continue. Staff can then see their payslips online, and the pay period's timesheets are marked as paid.

Download the ABA file before you lock: once the pay run is locked, the ABA file needs it unlocked. The ABA file pays from the pay cycle's Wage Bank Account. See ABNs and Pay Cycles.

Then:

• Click 2. Submit to ATO to lodge it. See Lodge a Pay Run.
• Click 4. Pay Super to pay super. See Paying Super.

Unlock a pay run

Click Complete Payrun, then Unlock. Click Download Backup, then Confirm Unlock.

Unlocking doesn't change what's been paid, super or STP. To pay more for a period you've already paid, use an ad hoc pay run instead.

Pay an ad hoc pay run

An ad hoc pay run pays a pay period again, outside the usual cycle, such as a missed bonus or a correction.

1. Click Ad Hoc Payrun, then the pay cycle.
2. Under Ad hoc, choose Ad hoc - Blank Payslips to add lines yourself, or Ad hoc - Full Payrun to work out pay from timesheets.
3. Under Staff, choose All Staff, Paid Staff or Select.
4. Choose the Year, Run and Payment Date, and click Payrun.

Pay run troubleshooting

Guides related to pay runs

• How Payroll Works
• Leave and Public Holidays
• Lodge a Pay Run