QuickBooks Payroll: Adding or Changing Pay Types Vexes Users

We are hearing from payroll administrators who cannot find where QuickBooks hides the settings for additional pay types. The task should be routine, but the path differs between QuickBooks Online Payroll and QuickBooks Desktop Payroll, and the fields change depending on whether the employee is hourly, salaried, or commission only.

The core payroll problem

The issue usually starts when a worker needs more than a single base pay line. An employer may want to add an overtime rate, a bonus, a commission, a reimbursement, or tip income. In QuickBooks Online, that setting lives in the employee profile, not in a global payroll settings menu. In QuickBooks Desktop, the same job begins in the Payroll Item List. Users who look in the wrong place often end up with duplicate items or pay runs that do not calculate the way they expect.

Symptoms users describe

Readers tell us about several recurring symptoms. A salaried employee cannot be given an hourly add-on, or the option appears missing. A new pay type is created but does not show up on the next pay run. An employee record shows the wrong compensation type, or the base pay fields do not match the worker’s terms. Others report that an old pay type remains visible on the employee profile and they cannot tell whether removing it will affect history.

QuickBooks Online: the settings path

The accepted answer resolves the Online side by starting from the employee record. Select the employee from the payroll employee list, then open the base pay section. There, choose whether the worker is hourly, salaried, or commission only. The fields that appear depend on that choice, so a salaried worker will show a salary and pay frequency, while an hourly worker will show a rate per hour and default working hours.

For additional pay types, the answer points to a separate section on the same employee screen. Use the add option to attach an existing pay type, or choose the new pay type option to create one. The detail fields change again based on the pay type, so a reimbursement item may ask for different information than an overtime item. After saving, the new line becomes part of that employee’s payroll record. The answer also notes a recent behavior change: an hourly pay type can now be added to an employee whose base pay is set to salary.

To edit an additional pay type, return to the same section and use the edit action next to the existing item. Changes are saved at the employee level rather than applied to every worker at once.

QuickBooks Desktop: setting up a pay item

In QuickBooks Desktop Payroll, the accepted answer starts with the payroll item list. Open that list from the Lists menu, choose to create a new payroll item, and select the wage category. The available wage types include hourly wages, annual salary, commission, and bonus. For hourly wages, the setup asks whether the item is regular or overtime pay.

Each item needs a name and an expense account so the payroll costs land in the correct place in the books. The answer calls out one exception: for a bonus pay item, leave the default rate field blank and enter the actual rate when the item is assigned to an employee. The final setup screens ask whether the earnings are insurable and which reporting period applies. After the item is finished, it can be applied to the relevant employee records.

Key details from the accepted answer

The main difference is where each product keeps the control. QuickBooks Online treats pay types as part of the employee profile, so edits affect one worker at a time. QuickBooks Desktop treats pay items as list entries that are created once and then assigned. That distinction explains much of the confusion.

The answer also makes clear that not every field appears for every pay type. Users should expect the form to change based on compensation type, hourly versus salary, and whether the item is overtime, bonus, commission, or a reimbursement. If a pay type is no longer used, the guidance is to handle it where it is assigned, at the employee level in Online or in the list in Desktop, rather than assuming a global delete will clean up past pay history.