Manage pay schedules and include terminated employees in pay runs

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the Add button.
5. Complete the following fields:
   • Name
     (The pay schedule name, along with the Employing Entity and date, will appear in the ABA bank file name downloaded from your platform. Avoid special characters and keep it short (248 characters max).)
   • Frequency
     • Weekly
     • Fortnightly
     • Monthly (Monthly Payment Mode appears when you select Monthly. It calculates an average number of hours per month for employees with advanced standard hours set up, instead of paying hours based on the number of days in each month.)

   • Included employees

     Important

     In the Included employees field, if you select Employees with this pay schedule as their default, your pay runs will include an Include terminated employees checkbox.

     Ticking this checkbox when creating a pay run allows you to include employees who have a termination date within the selected pay period.

     NZ-Specific: IRD Number Configuration

     For New Zealand users, the Included employees field is critical for IRD compliance. It must be set to "Employees with this pay schedule as their default and employed by the following employing entity" to ensure the pay run reports to the correct IRD number. This is especially important for off-cycle schedules, which are often misconfigured and can inadvertently send filings to the wrong IRD number. If not configured correctly, you may receive IRD payday filing errors such as "The IRD has no record of [employee]".

     If your business has multiple employing entities, set up separate pay schedules for each entity (e.g., "Fortnightly – Entity 1," "Fortnightly – Entity 2") to simplify IRD compliance and IR345 reporting splits.

   • Pay run warnings (Refer to this article's Further information section for details on pay run warnings.)
   • PAYE payments (Australia):
     • Account name
     • NZ bank account number
     • Account number
     • Reference

   • IRD payments (New Zealand):

     IRD Settings Configuration

     Before setting up IRD payment details on a pay schedule, ensure that IRD Settings have been configured under Business Settings → Payroll Settings. These settings are required to enable payday filing and must be configured separately for each employing entity if your business has multiple entities.

     Reference article: Configure Inland Revenue Department (IRD) settings as an employer on Payroll.

     • Account name
     • Account number
     • Reference

     IRD Deductions and Payment Processing

     Normal deductions such as PAYE, KiwiSaver, Student Loan, and ESCT are reported to IRD via payday filing and are paid as part of the standard pay run process. Always use system-default deduction categories, as custom deduction categories may not report correctly to IRD, even if the amount is correctly deducted from the employee.

     Tax arrears payments are different: since they are not reported via payday filing, they must be paid separately to a bank account set up on the employee's bank details screen, not bundled into the standard IRD payment.

     IRD payments and bank file limits: IRD payments can be included as part of the bank file for a pay run. Be aware that when IRD payments are included in the same bank file as wages, the total payment amount may exceed the $10,000 threshold, which can be relevant to certain banking or payment processing limits. Some banking tiers do not support IRD payments via bank file at all — check with your bank if you encounter limitations.

6. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be automated.
5. Under Pay run automation, click the edit button.

6. Complete the required fields on the Auto Pay Schedule Details page.

   Important

   Select the Include terminated employees checkbox to automatically include employees who ended employment during the selected pay period. This ensures their final pay is processed.

   Otherwise, leave the checkbox unticked to include only active employees.

7. Click the Next button.
8. Set the required Warnings and Notifications that need to be enabled. (Refer to this article's Further information section for details on pay run warnings.)
9. Click the Next button.
10. In the Finalise pay run field, select the required checkbox.
11. Click the Next button.
12. Click the Complete button.
13. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be edited.

5. Make the required changes in the field(s) you need to edit.

   Helpful Hint

   To include terminated employees in future pay runs, click the drop-down button in the Included employees field and select Employees with this pay schedule as their default.

   This will ensure the Include terminated employees checkbox appears in future pay runs for your selected schedule.

6. Click the Save button.

To update an individual employee's pay schedule:

1. Go to the Employee's Pay Default Screen.
2. Select the employee whose pay schedule needs to be changed.
3. Choose the desired pay schedule from the dropdown or list.
4. Save the changes.

Important: When changing an employee's pay schedule, remember that the first pay run after the change may require manual adjustments. This is because the pay run will apply to the full period, which might include a period already paid under the previous schedule. Only the first month/week will require these manual amendments.

Syncing with the HR Platform: Any changes made to pay schedules need to be synced with your HR platform. Refer to the support article on updating pay schedules via the HR platform for detailed instructions on syncing.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be paused.
5. Click the Pause button.
6. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be resumed.
5. Click the Resume button.
6. Click the Save button.

The first step is to create the new pay schedule in Payroll. If you have Employment Hero HR, this will automatically sync back to HR and be available to assign to your employees.

HR platform changes

If your organisation uses both the HR and Payroll platforms, certain changes must be made in each platform separately.

To update employee records in the HR platform:

1. Export your employee data.
2. Keep a copy of the original file before making any changes.
3. Make the required changes in the copied file.
4. Import the updated employee data.

The following items will need to be updated in the HR platform:

• Pay Details (salaried employees) — Review how each salaried employee's pay is configured (e.g. annual, monthly). If a change is needed, add a new salary record effective from the start date of the first pay run under the new frequency, once the last pay run under the old frequency has been finalised.
• Bank Details (employees with split payments) — If any employees have fixed-amount bank splits (rather than percentage-based), these may need to be adjusted to reflect the new pay frequency.

Payroll platform changes

Deductions

• Child Support Deductions / Garnishees — Contact Services Australia to update the pay cycle frequency. New letters will be issued, and deduction amounts and protected earnings amounts will need to be updated to match the new pay frequency.
• Salary Sacrifice to Super — Check with affected employees whether their ongoing deduction amount needs to change (for example, a $40 monthly contribution may become $20 per fortnight). If you are running an interim payroll to bridge the change in pay period, discuss with employees how salary sacrifice will be treated in that pay run.
• Ongoing Tax Adjustments — If employees have requested an additional tax withholding amount, contact them to confirm whether this should also be updated. Note: this does not apply to STSL calculations or withholding variations issued by the ATO.
• Deductions to third-party providers — Contact each relevant provider to confirm the change in pay frequency. New deduction amounts may be issued, and you will need to report these updated amounts to the providers. This includes:
  • Novated leases
  • Salary packaging arrangements
  • Workplace giving

Allowances

Review any fixed allowances paid each pay run (such as a car allowance) and convert them to the new frequency. For example, a car allowance of $120.00 per month would become $55.39 per fortnight.

Instructions for updating payrun inclusions

1. Export current pay run inclusions using the Monthly Payrun Inclusion Report.
2. Export a file template by going to Payroll Settings to help with importing employee deductions in bulk.
3. Make the necessary changes to the file.
4. Import the updated employee changes.

Updating employee details

Note: The following steps apply to changes made in the Payroll platform only, not changes made in HR.

1. Export the Employee Details Report.
2. Keep a copy of the original data before making any changes.
3. Make the required changes in the copied file.
4. Import the updated employee data.

Additional considerations

• Bank Account Splits — If employees split their pay across more than one bank account using fixed amounts, discuss with them whether those amounts need to change once the pay frequency is updated.
• Overtime — If there is an interim period during the pay cycle change, consider how to treat any applicable overtime to ensure employees are not disadvantaged.
• Salaried employees — Check how your system handles salaried or autopay employees under the new frequency. For example, a full-time employee may move from 164.67 hours per month to 76 hours per fortnight.
• Rulesets — Review any monthly or salaried rulesets that need to be converted to the new frequency, or move employees to the correct ruleset. If a new ruleset is required, a copy of the existing ruleset can be created so changes are made to the copy rather than the original.
• Rosters — If your organisation uses rosters, review whether any roster configurations need to be updated to reflect the new pay frequency.
• Tasks — Review any pay run tasks that may need to be amended.
• Leave Allowance Templates (LATs) — Review any monthly LATs and either convert them to the new frequency or move employees to the appropriate LAT.
• Report Packs — Update any report packs to reflect the new pay frequency.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be stopped.
5. Click the Stop button.
6. Click the Delete button.
7. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the Delete button.
5. In the Confirm delete? window, click the Delete button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the Add button.
5. Complete the following fields:
   • Name
     (The pay schedule name, along with the Employing Entity and date, will appear in the ABA bank file name downloaded from your platform. Avoid special characters and keep it short (248 characters max).)
   • Frequency
     • Weekly
     • Fortnightly
     • Monthly (Monthly Payment Mode appears when you select Monthly. It calculates an average number of hours per month for employees with advanced standard hours set up, instead of paying hours based on the number of days in each month.)

   • Included employees

     Important

     In the Included employees field, if you select Employees with this pay schedule as their default, your pay runs will include an Include terminated employees checkbox.

     Ticking this checkbox when creating a pay run allows you to include employees who have a termination date within the selected pay period.

     NZ-Specific: IRD Number Configuration

     For New Zealand users, the Included employees field is critical for IRD compliance. It must be set to "Employees with this pay schedule as their default and employed by the following employing entity" to ensure the pay run reports to the correct IRD number. This is especially important for off-cycle schedules, which are often misconfigured and can inadvertently send filings to the wrong IRD number. If not configured correctly, you may receive IRD payday filing errors such as "The IRD has no record of [employee]".

     If your business has multiple employing entities, set up separate pay schedules for each entity (e.g., "Fortnightly – Entity 1," "Fortnightly – Entity 2") to simplify IRD compliance and IR345 reporting splits.

   • Pay run warnings (Refer to this article's Further information section for details on pay run warnings.)
   • PAYE payments (Australia):
     • Account name
     • NZ bank account number
     • Account number
     • Reference

   • IRD payments (New Zealand):

     IRD Settings Configuration

     Before setting up IRD payment details on a pay schedule, ensure that IRD Settings have been configured under Business Settings → Payroll Settings. These settings are required to enable payday filing and must be configured separately for each employing entity if your business has multiple entities.

     Reference article: Configure Inland Revenue Department (IRD) settings as an employer on Payroll.

     • Account name
     • Account number
     • Reference

     IRD Deductions and Payment Processing

     Normal deductions such as PAYE, KiwiSaver, Student Loan, and ESCT are reported to IRD via payday filing and are paid as part of the standard pay run process. Always use system-default deduction categories, as custom deduction categories may not report correctly to IRD, even if the amount is correctly deducted from the employee.

     Tax arrears payments are different: since they are not reported via payday filing, they must be paid separately to a bank account set up on the employee's bank details screen, not bundled into the standard IRD payment.

     IRD payments and bank file limits: IRD payments can be included as part of the bank file for a pay run. Be aware that when IRD payments are included in the same bank file as wages, the total payment amount may exceed the $10,000 threshold, which can be relevant to certain banking or payment processing limits. Some banking tiers do not support IRD payments via bank file at all — check with your bank if you encounter limitations.

6. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be automated.
5. Under Pay run automation, click the edit button.

6. Complete the required fields on the Auto Pay Schedule Details page.

   Important

   Select the Include terminated employees checkbox to automatically include employees who ended employment during the selected pay period. This ensures their final pay is processed.

   Otherwise, leave the checkbox unticked to include only active employees.

7. Click the Next button.
8. Set the required Warnings and Notifications that need to be enabled. (Refer to this article's Further information section for details on pay run warnings.)
9. Click the Next button.
10. In the Finalise pay run field, select the required checkbox.
11. Click the Next button.
12. Click the Complete button.
13. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be edited.

5. Make the required changes in the field(s) you need to edit.

   Helpful Hint

   To include terminated employees in future pay runs, click the drop-down button in the Included employees field and select Employees with this pay schedule as their default.

   This will ensure the Include terminated employees checkbox appears in future pay runs for your selected schedule.

6. Click the Save button.

To update an individual employee's pay schedule:

1. Go to the Employee's Pay Default Screen.
2. Select the employee whose pay schedule needs to be changed.
3. Choose the desired pay schedule from the dropdown or list.
4. Save the changes.

Important: When changing an employee's pay schedule, remember that the first pay run after the change may require manual adjustments. This is because the pay run will apply to the full period, which might include a period already paid under the previous schedule. Only the first month/week will require these manual amendments.

Syncing with the HR Platform: Any changes made to pay schedules need to be synced with your HR platform. Refer to the support article on updating pay schedules via the HR platform for detailed instructions on syncing.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be paused.
5. Click the Pause button.
6. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be resumed.
5. Click the Resume button.
6. Click the Save button.

The first step is to create the new pay schedule in Payroll. If you have Employment Hero HR, this will automatically sync back to HR and be available to assign to your employees.

HR platform changes

If your organisation uses both the HR and Payroll platforms, certain changes must be made in each platform separately.

To update employee records in the HR platform:

1. Export your employee data.
2. Keep a copy of the original file before making any changes.
3. Make the required changes in the copied file.
4. Import the updated employee data.

The following items will need to be updated in the HR platform:

• Pay Details (salaried employees) — Review how each salaried employee's pay is configured (e.g. annual, monthly). If a change is needed, add a new salary record effective from the start date of the first pay run under the new frequency, once the last pay run under the old frequency has been finalised.
• Bank Details (employees with split payments) — If any employees have fixed-amount bank splits (rather than percentage-based), these may need to be adjusted to reflect the new pay frequency.

Payroll platform changes

Deductions

• Child Support Deductions / Garnishees — Contact Services Australia to update the pay cycle frequency. New letters will be issued, and deduction amounts and protected earnings amounts will need to be updated to match the new pay frequency.
• Salary Sacrifice to Super — Check with affected employees whether their ongoing deduction amount needs to change (for example, a $40 monthly contribution may become $20 per fortnight). If you are running an interim payroll to bridge the change in pay period, discuss with employees how salary sacrifice will be treated in that pay run.
• Ongoing Tax Adjustments — If employees have requested an additional tax withholding amount, contact them to confirm whether this should also be updated. Note: this does not apply to STSL calculations or withholding variations issued by the ATO.
• Deductions to third-party providers — Contact each relevant provider to confirm the change in pay frequency. New deduction amounts may be issued, and you will need to report these updated amounts to the providers. This includes:
  • Novated leases
  • Salary packaging arrangements
  • Workplace giving

Allowances

Review any fixed allowances paid each pay run (such as a car allowance) and convert them to the new frequency. For example, a car allowance of $120.00 per month would become $55.39 per fortnight.

Instructions for updating payrun inclusions

1. Export current pay run inclusions using the Monthly Payrun Inclusion Report.
2. Export a file template by going to Payroll Settings to help with importing employee deductions in bulk.
3. Make the necessary changes to the file.
4. Import the updated employee changes.

Updating employee details

Note: The following steps apply to changes made in the Payroll platform only, not changes made in HR.

1. Export the Employee Details Report.
2. Keep a copy of the original data before making any changes.
3. Make the required changes in the copied file.
4. Import the updated employee data.

Additional considerations

• Bank Account Splits — If employees split their pay across more than one bank account using fixed amounts, discuss with them whether those amounts need to change once the pay frequency is updated.
• Overtime — If there is an interim period during the pay cycle change, consider how to treat any applicable overtime to ensure employees are not disadvantaged.
• Salaried employees — Check how your system handles salaried or autopay employees under the new frequency. For example, a full-time employee may move from 164.67 hours per month to 76 hours per fortnight.
• Rulesets — Review any monthly or salaried rulesets that need to be converted to the new frequency, or move employees to the correct ruleset. If a new ruleset is required, a copy of the existing ruleset can be created so changes are made to the copy rather than the original.
• Rosters — If your organisation uses rosters, review whether any roster configurations need to be updated to reflect the new pay frequency.
• Tasks — Review any pay run tasks that may need to be amended.
• Leave Allowance Templates (LATs) — Review any monthly LATs and either convert them to the new frequency or move employees to the appropriate LAT.
• Report Packs — Update any report packs to reflect the new pay frequency.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the pay schedule that needs to be stopped.
5. Click the Stop button.
6. Click the Delete button.
7. Click the Save button.

1. On the main menu, click Business.
2. On the submenu, click Payroll Settings.
3. Under Pay Run Settings, click Pay Schedules.
4. Click the Delete button.
5. In the Confirm delete? window, click the Delete button.