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How to run payroll

The helpline for support on QuickBooks India payroll has changed to 080 3959 1100. This helpline will be operational from Monday to Friday, 9:30 AM to 6:00 PM.

Prior to Run Payroll, ensure that you have updated employee creations, master changes and salary revisions if any.

  1. To run payroll, click the Employees tab from the left navigation and then click Run Payroll at the top right of the page.
    Note: Run Payroll 6-step flow. The flow that you are on will have its number shaded in blue. The rest will be greyed out.
  2. Select the location(s) to process payroll for. If there is only one location, it will be selected by default and you'll automatically move to the next tab.
  3. Click Next to enter Attendance details.
  4. Click the + sign to enter employee wise Loss of Pay details manually.
  5. Click the arrow icon to upload attendance in bulk.
    • Updated Loss of Pay details will be accounted for salary calculations for the month against standard working days.
    • Loss of Pay details can be accounted automatically in column FROM-LMS if the Leave Management module is enabled.
    • Loss of Pay details can be accounted automatically in column FROM-ATTENDANCE if Biometric attendance is integrated with the Leave Management module.
    • Depending on the biometric attendance rule configuration, Late Occurrence can be calculated and used for appropriate salary calculations.
  6. Click Next to enter Pay Adjustment details.
  7. To update variable payments like incentives, shift allowances, bonus etc., double-click the employee grid to edit existing records.
  8. Click the + sign to enter employee wise/component wise pay details manually.
  9. Click the arrow to upload bulk Pay Adjustment details using an excel sheet.
  10. Click Next to select employees to Run Payroll.
  11. Click Next to confirm payroll output.
  12. Double-click an employee in the employee grid to view employee pay details and click the Back button to correct or update additions in payroll.
  13. Click Next to complete payroll.
  14. If needed, click Download Salary Register.
  15. Select Lock payroll and Post JV entry to post a journal entry to QuickBooks.
  16. Click Done to finalise payroll for the month.


  • Clicking Done without checking Lock payroll and Post JV entry processes the payroll, but does not post an accounting entry to QuickBooks.
  • Payroll cannot be reprocessed until you unlock payroll once the journal entry is posted. To unlock the current payroll, go to the Employees page and click the drop-down arrow next to Run Payroll and select Unlock payroll. Unlock payroll can be done for the current processed payroll only and will not allow to unock of prior months.
  • Select the latest payroll period from the Month drop-down, remove the tick from the relevant location and then click Save. This process will delete the journal entry that was posted to QuickBooks. Once done, payroll can be reprocessed.
  • After you run payroll, go to Reports to generate salary reports and statutory/compliance reports.

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