Payroll Help

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How to Pay Salaried Employees in Payroll

In this article:

How to Pay Employees with a Salary

  1. Go to Payroll > Run a New Payroll.
    • On payroll Step 1: Payroll Entry, all active salaried employees will appear in the employee list.
  2. Under the “Pay Salary” column, each salaried employee will have a checkbox.
    • This checkbox is automatically selected, meaning the employee’s full flat-dollar salary will be included in payroll.
    • To exclude a salaried employee from receiving their regular pay, simply uncheck the box.
  3. Add Hours
    • If your state requires payroll hours for reporting or if you have set up time off accrual rules, hours will be mandatory.
    • 💡 Salaried employee pay does not change based on the hours entered.
  4. Add extra pay as needed (e.g., bonuses or additional earnings) in addition to their regular salary.
    • Use the “Off Cycle Payroll” in the Pay Schedule drop down to pay salaried employees ONLY a bonus or payroll that is not in the normal payroll run. See our help article, “How to Run an Off-cycle Payroll,” for more info.

Paying a Partial Salary

If an employee took unpaid time off and should receive a reduced salary, you have two options:

Option 1: Temporarily Adjust the Salary Rate

  1. Go to the employee’s Pay Info tab. Payroll > Employee list > {select the employee name} > Pay Info.
  2. Edit their salary to reflect the lower amount.
  3. Run payroll.
  4. After payroll is complete, change the salary back to the original amount.

Option 2: Use a Custom Money Type

  1. Create a new Money Type specifically for partial salary payments. Settings > Payroll > Hours and Money Types.
  2. Click +Add New
  3. Name your money type something that will allow you and the employee to easily identify it, ex: “Partial Salary.”
  4. In payroll:
    • Uncheck the “Pay Salary” box to prevent full salary payment.
    • Enter the partial salary amount in the custom Money Type field.

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