Processing your payroll

You'll do a pay run whenever you want to pay your employees – usually at a set frequency (pay cycle) like weekly, fortnightly or monthly.

When you do a pay run, you're guided through each step so nothing gets missed. Your employees' regular pay amounts will be included, but you can easily make changes, like adding leave or adjusting hours.

Payroll at a glance

Here are the basic steps for paying your employees (Create menu > Pay run).

1. Select pay period to choose who you're paying and the dates they're being paid for.

2. Calculate pays to make changes or additions, like leave or adjusted hours.

3. Record and report to confirm who and what you're about to pay, and declare the pay to the ATO.

4. Prepare pay slips to email or print for your employees.

5. Done! Finish the job by paying your employees into their bank accounts.

A pay run in detail

Start a new pay run via the Create menu > Pay run.

1. Select pay period

1. Choose the Pay cycle for the employees you want to pay. This will be remembered for the next pay run so you won't have to choose it every time. If the pay isn't part of a typical pay cycle, like a one-off bonus, choose Unscheduled. More about unscheduled pays.

2. Confirm the Pay period start and Pay period end dates.

3. Confirm the Date of payment.

   • This is the date you'll make the payments to your employees, and the payment date that shows on pay slips.

   • This date determines the financial year the pay falls into, regardless of the pay period. For example, if the date of payment is June 30 the entire pay falls into the June financial year.

   • If you enter a future date, the pay will be recorded in MYOB on the day you complete the pay run. If you pay employees using a bank (ABA) file, it's the date you want your bank to process the payments.

   • If you enter a past date, you'll need to choose how to report the pay for STP.

4. If any timesheets have been recorded for this pay period, they'll be listed and selected. Deselect any timesheets you don't want to include in this pay run.

   • If timesheets aren't showing, check the right pay cycle is chosen and if the timesheet hours have already been paid. How to check these things.

5. When you're done, click Next.

2. Calculate pays

At the Calculate pays step of the pay run, you'll see the employees you're paying. To be included in the pay, an employee's pay cycle must match the one chosen at the previous step, e.g. Weekly. Check an employee's pay cycle in their record (Payroll > Employees > click the employee > Payroll details tab > Salary and wages tab > Pay cycle).

1. Deselect any employees you don't want to include in this pay.

2. Click an employee to see the details of their pay or make any changes.

   Changing hours worked

   You may need to change the hours worked by an employee if they're not being paid for a full standard pay period, for instance, if their work hours vary.

   Changing the hours worked only affects this pay. If you need to permanently change an employee's regular hours, update it in their standard pay.

   If you edit an employee’s hours during the pay run, any adjustments you make will not update hours entered on timesheets or timesheet reports.

   1. At the Calculate pays step of the pay run, click the employee to expand their pay.

   2. Change the hours worked for the applicable wage pay item. For example, enter a casual worker's actual hours worked against the Base Hourly pay item.

   3. Click the employee again to collapse their pay.

      

   Adding leave

   If an employee has been set up for leave you'll be able to add the leave taken on their pay.

   Leave without pay

   If entering leave without pay, reduce the employee's normal hours by the number of hours of unpaid leave. Otherwise they'll be overpaid.Learn more about leave without pay.

   1. At the Calculate pays step of the pay run, click the employee to expand their pay.

   2. Enter the number of hours of leave against the applicable leave pay item. For example, enter annual leave hours against Annual Leave Pay.

   3. If you've set up the leave pay item with the option Automatically adjust base hourly or base salary details selected, the employee's Base Salary or Base Hourly amount will be automatically reduced to cater for the leave payment. Otherwise you'll need to adjust this manually to avoid overpayment.

   4. (Optional) Hover over the info  icon in the leave hours field to see the employee's leave balance details.

   5. (Optional) Use the Pay slip message field in the employee's pay to enter their leave dates. Here's our example showing 7.6 hours annual leave added to the pay with leave balance details shown.

      

   6. Click the employee again to collapse their pay.

   Negative leave balances

   If an employee takes more leave than they've accrued, their leave balance will become negative. However, they'll still be paid for all the leave entered on the pay run.

   Including other payments like overtime, allowances or deductions

   Include additional payment types like overtime, allowances or deductions during the pay run. If the additional payment is the same amount each pay, automate the payment by adding it to the employee's standard pay.

   If other types of payments have been included on a timesheet, you don't need to use this procedure.

   1. At the Calculate pays step of the pay run, click the employee to expand their pay.

   2. Enter the payment or deduction in the Hours or Amount fields next to the applicable pay item. For example, to pay 3 hours of overtime, enter 3 hours against the applicable overtime pay item.

      

   3. If the payment type isn't listed, click Add wage or Add deduction to add it. You can only add a pay item this way if there's already at least one of the same type of pay item in the pay. Otherwise, here's how to assign pay items to employees.
      

   4. Click the employee again to collapse their pay.

   The same approach can be used if a regular allowance or deduction amount changes or isn't required for a pay. Just change (or remove) the allowance or deduction Hours or Amount in the pay.

   
   
   

   Assigning jobs to pay amounts

   Jobs can be assigned to pay item amounts to track the wage expense of work performed on that job. You can assign one or more jobs to each pay item.

   1. At the Calculate pays step of the pay run, click the employee to expand their pay.

   2. Click Add job next to the corresponding pay item.

   3. Select one or more jobs.

   4. Add the amount to be allocated to each selected job.

   5. Click Add.

   6. Click the employee again to collapse their pay.

      

   You can also assign a default job to an employee in their standard pay. 

   Adding a message to the pay slip

   You can enter a default pay slip message in an employee's standard pay that'll appear on all pay slips for that employee. But you can update this message or enter a new one during the pay run, and it'll only appear on the pay slip for this pay.

   1. At the Calculate pays step of the pay run, click the employee to expand their pay.

   2. Enter or update the Pay slip message.

      

   3. Click the employee again to collapse their pay.

3. When you're done, click Next.

3. Record and report

1. Review the pays you're about to record. Check the previous and current pay amounts to easily identify any variances.

2. To verify who you're paying and what you're paying them in this pay run, you can click to generate these reports:

   • Preview pay run activity – shows a detailed list of salary and wages, taxes, deductions, leave, and expenses for this pay run

   • Preview pay details – shows the Payroll verification report containing a summary of each employee's pay in this pay run

3. When you're ready, click Record.

4. When prompted to send payroll information to the ATO (for Single Touch Payroll reporting), enter the name of the authorised sender and click Send.

4. Prepare pay slips

1. On the Email pay slips tab, select the employees requiring their pay slips to be emailed then click Email pay slips. Need to change an employee's pay slip delivery method?

2. On the Print pay slips tab, click View PDF for an employee to open the pay slip as a PDF in a new window. You can now save or print the pay slip.

3. When you're done, click Next.

5. Done!

The pay run is recorded and you can now prepare to pay into your employees' bank accounts by clicking Pay employees via electronic payments.

To view your Single Touch Payroll reports to make sure they've been accepted by the ATO, click Payroll reporting (STP). Help me fix a rejected STP report.

Managing payroll, reporting and super

Here are some other key tasks to help manage your payroll.

Check your STP reports

Make sure the ATO accept the reports you send them after each pay. View STP reports

Make super payments

Send payments to your employees' super funds at least quarterly. Make super payments

Adjust a pay

You can fix most pay issues in the next pay run or a separate pay. Fix a pay

Review payroll reports

All your payroll info at a glance, including paid and accrued leave and super. Review payroll reports