QuickBooks Online Payroll handles unscheduled pay runs through the “Run payroll” dropdown on the Employees page, where you can choose a bonus-only, commission-only, or fringe-benefits-only payroll outside your regular schedule. The process takes just a few minutes once you know where to click, but getting the timing and tax settings right matters if you want employees paid on the date you intend.
When You’d Run an Unscheduled Payroll
An unscheduled payroll is any pay run that falls outside your normal payroll schedule. The most common reasons include paying a one-time bonus, issuing a commission check, correcting a missed payment, paying out accrued PTO for a departing employee, or distributing fringe benefits. QuickBooks Online treats these as separate payroll types so the taxes calculate correctly and the payment doesn’t get tangled with your next regular run.
Step-by-Step: Running an Off-Cycle Payroll
Start by navigating to All Apps, then Payroll, then Employees. On that screen, look for the “Run payroll” dropdown button. Instead of selecting your regular pay schedule, choose one of the off-cycle options: Bonus only, Commission only, or Fringe benefits only.
QuickBooks may ask follow-up questions depending on your selection, such as how you want taxes calculated. Answer those prompts and select Continue. On the next screen, set or confirm the pay period dates and pay date, then check the boxes next to the employees you want to include in this run.
For each selected employee, click the Actions menu (the three-dot icon) and choose “Edit paycheck” to enter specific amounts, hours, memos, or other details. If you use QuickBooks Time for tracking, you can pull in approved hours from there as well.
Once everything looks right, select Preview payroll. On the preview screen, confirm the bank account QuickBooks will use to fund the payroll. Then select “Preview payroll details” for a final review. From there you can either submit the payroll immediately or save it for later if you need approval from someone else first. Hit Close when you’re done.
Paying a Bonus With Supplemental Tax Rates
When you choose the “Bonus only” option from the Run payroll dropdown, QuickBooks asks how you want to enter the bonus amount. You have two choices:
- As a net amount: The employee receives the exact dollar figure you enter. QuickBooks still calculates the taxes owed, but you (the employer) cover them on top of the stated bonus.
- As a gross amount: QuickBooks calculates federal and state withholding from the bonus and the employee receives whatever is left after taxes.
For either option, QuickBooks applies federal and state supplemental tax rates by default, which is the recommended approach. The federal supplemental rate is a flat percentage applied to bonus and commission payments rather than the employee’s regular withholding rate. This keeps the tax calculation clean and avoids the over-withholding that sometimes happens when a large bonus gets lumped into a regular paycheck.
Choosing Paper Check or Direct Deposit
If you need to hand an employee a physical check rather than sending a direct deposit, you can switch the payment method during the payroll run itself. After selecting the employee on the payroll screen, look for the “Pay method” column in that employee’s row. Change the dropdown from direct deposit to “Paper check.” Then preview and submit the payroll as usual. QuickBooks will record the transaction and calculate the taxes, but it won’t initiate an electronic transfer for that employee.
This is useful when you’ve already handed someone a paper check and need to document it in the system, or when you need to pay someone faster than your direct deposit lead time allows.
Direct Deposit Lead Times
Unscheduled payrolls follow the same direct deposit timing rules as your regular runs, and missing the cutoff means your employees won’t get paid on the date you selected. The lead time depends on your QuickBooks Online Payroll plan level.
The Core plan offers two-day and five-day funding windows. Premium and Elite plans add a one-day option. Same-day direct deposit, where available, requires submission before 7:00 AM Pacific Time on the pay date itself. For next-day deposits, the deadline is 5:00 PM Pacific the day before payday. Two-day deposits must be submitted by 5:00 PM Pacific two banking days before payday.
A few rules apply to all plans. Direct deposits only process on banking days, so weekends and federal or state holidays don’t count toward lead time. If your payday is a Monday, for example, a two-day lead time means submitting by 5:00 PM Pacific the prior Thursday. You also need sufficient funds in your linked bank account on the day you submit. If the payroll amount exceeds your direct deposit limit, you can temporarily switch to the five-day funding window to process it.
After You Submit
Once the payroll is submitted, QuickBooks calculates and files the associated payroll taxes automatically (assuming your plan includes that feature). The payment will appear on the employee’s next pay stub and in your payroll reports. If you need to make a correction after submitting, you can void the paycheck and rerun it, but acting quickly matters since QuickBooks may have already initiated the direct deposit or tax payment.
To verify everything went through, go back to the Payroll section and check the payroll history. Each off-cycle run appears as its own entry, separate from your scheduled payrolls, making it easy to track bonus and commission payments at tax time or during an audit.