How to Create a One-Time Payroll Check in QuickBooks Online

Creating a one-time payroll check in QuickBooks Online is a straightforward process. Whether you're paying a bonus, severance pay, or issuing a last-minute check, QuickBooks Online Payroll offers an easy-to-follow system to handle it. This guide will walk you through the steps, the considerations to keep in mind, and some tips to ensure accuracy.

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1. Understanding One-Time Payroll in QuickBooks Online

A one-time payroll check typically refers to a payment that isn't part of the regular payroll cycle. Examples of one-time payroll checks include:

Bonus payments
Severance pay
Commissions
Pay adjustments
Miscellaneous one-time payments

Each of these payments may have different tax implications and deductions, so it’s important to correctly set them up in QuickBooks Online Payroll.

2. Types of One-Time Payroll Payments

Before setting up a one-time payroll check, you should understand the various types of payments and when they are appropriate:

Bonuses: These are typically performance-based payments that are issued outside the regular payroll schedule.
Severance Pay: Offered when an employee leaves the company, either voluntarily or involuntarily, and it is essential to handle the associated taxes properly.
Commissions: If employees earn based on sales or specific actions, their commission may be a one-time payment, depending on when and how often it is paid.
Overtime/Back Pay: Employees may receive an additional payment for overtime worked or for back pay owed from previous periods.

Now, let’s explore the step-by-step guide to creating these one-time payments in QuickBooks Online.

3. Preparing to Create a One-Time Payroll Check

Before you can create a payroll check in QuickBooks Online, a few important preparation steps are required:

a. Ensure Payroll Setup is Complete

To issue a one-time payroll check, you must have the QuickBooks Online Payroll service enabled. If you haven’t set it up already, follow the steps:

Go to the Settings (gear icon) on your QuickBooks Online dashboard.
Under Your Company, select Payroll Settings.
Follow the prompts to activate payroll, set up employees, and link your business bank account for payroll payments.

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b. Check Employee Status

Ensure the employee you are paying is correctly set up in the system. Even if the payment is a one-time occurrence, the employee should be added to your payroll.

Go to the Employees tab under the Payroll menu.
If the employee isn't listed, click on Add an employee and input their details, such as name, address, salary, and tax information.

c. Understand Payroll Tax Settings

One-time payments such as bonuses or severance checks often have different tax implications compared to regular wages. QuickBooks Online automatically calculates federal and state taxes, but you should review the settings to ensure compliance with the IRS guidelines for supplemental wages.

4. Step-by-Step Guide to Creating One-Time Payroll Checks

Once the preparations are in place, you’re ready to create the payroll check. Follow these detailed steps:

a. Access Payroll

Log in to QuickBooks Online.
From the left-hand navigation bar, click on Payroll.
Select Employees.

b. Choose the Employee

In the Employees tab, select the employee you want to pay.
Click on their name to view their payroll details.

c. Run Payroll for One-Time Payment

Once you’re in the employee’s profile, click on the Run payroll option.
Choose the Off-cycle Payroll or Bonus Payroll option. This option allows you to run a payroll outside of your regular pay schedule without affecting your scheduled payroll runs.

d. Enter Payment Details

Under the payment type, choose Bonus, Commission, Severance, or the appropriate category for your one-time payment.
Input the gross amount you want to pay. Ensure you understand if the gross amount is pre-tax or post-tax, as this will affect the calculation.
Check and adjust any pre-tax deductions (if applicable).

e. Verify Tax Withholding

QuickBooks Online will calculate taxes based on your settings and employee data. Review these taxes carefully, especially for supplemental payments like bonuses, which may have different tax rates.
If necessary, make adjustments to the federal or state withholding by clicking the Tax settings link on the payroll page.

f. Set the Payment Method

QuickBooks allows you to choose between direct deposit and paper checks. If your employee is set up for direct deposit, select this option.
If you prefer to issue a paper check, choose the Paper Check option and make a note to print the check or issue it manually.

g. Review and Submit

Review the entire payroll details, including the employee’s gross pay, taxes, deductions, and net pay.
Click Submit to finalize the payroll check.

5. Handling Special Cases: Bonuses, Severance, and Commissions

Special one-time payments such as bonuses, severance, and commissions may have additional considerations.

a. Bonuses

When issuing bonuses, it’s important to decide whether the bonus is taxed at a flat rate or combined with regular wages. In most cases, bonuses are taxed as supplemental wages and follow a federal withholding rate of 22% (as of 2024). QuickBooks automatically calculates this tax for you.

b. Severance Pay

Severance pay requires special attention to tax implications, as well as state-specific laws. Ensure that QuickBooks applies the correct state taxes, especially for multi-state employees.

c. Commissions

Commissions can either be combined with regular payroll or processed as a one-time check. Be sure to review how your company tracks commissions to ensure accuracy in payment calculations.

6. Using Manual Payroll Check Option in QuickBooks Online

In cases where you prefer not to use the automated payroll feature, or for truly unique payments, QuickBooks allows you to manually issue a payroll check. This is a less common method but may be necessary in special circumstances.

a. Create a Manual Payroll Check

Go to Employees > Paycheck List > Create Paycheck.
Enter the gross amount, taxes, and any deductions manually.
Print the check or record the payment as a paper check.

While this option bypasses some automatic features of QuickBooks Online Payroll, it gives you more control over each payment detail.

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7. Adjusting for Additional Deductions

If the employee receiving the one-time payroll check has additional deductions, such as retirement contributions, health insurance, or wage garnishments, these will be automatically applied unless you manually exclude them. Here’s how to adjust deductions:

Navigate to Employee Settings: Go to the employee’s profile in the Employees tab.
Adjust Deductions: Under deductions, uncheck or edit the fields for any specific deductions that should not apply to this one-time payroll check.
Confirm Deductions: Ensure that only applicable deductions, such as federal taxes or FICA, are calculated before submitting payroll.

8. Recording Payroll Liabilities and Taxes

After running payroll, QuickBooks Online automatically tracks payroll liabilities and tax payments. To ensure compliance and timely filing:

Go to Payroll > Taxes.
Review the outstanding liabilities, such as payroll taxes, and record when they are due.
Set up automatic tax payments if your business opts for it to avoid missing deadlines.

9. Reporting One-Time Payroll Checks

QuickBooks Payroll Support Online offers various payroll reports to help you keep track of all payments, including one-time payroll checks. These reports ensure that all payments are correctly documented and help during tax season:

a. Payroll Summary Report

Access by navigating to Reports > Payroll Summary.
Select the relevant date range, ensuring the one-time payroll check falls within this period.
Review total payroll expenses, taxes, and other relevant data.

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b. Employee Pay Report

This report helps you monitor individual employee payments, including one-time checks.
Access it under Reports > Employee Pay.

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c. Tax Liability Report

Review the Tax Liability Report to ensure all withholdings and tax payments are properly documented.

10. Troubleshooting Common Issues with One-Time Payroll

While QuickBooks Online simplifies payroll, occasional issues can arise. Here are common challenges and how to address them:

a. Incorrect Tax Withholding on Bonus/Severance

If taxes are not withheld correctly, double-check:

Federal withholding rates (QuickBooks should use the supplemental wage rate for bonuses).
Employee tax settings in QuickBooks.

b. Direct Deposit Delays

Direct deposit issues can occur if banking details are incorrect or payroll processing times aren’t followed. Always review payment processing times before submitting.

c. Payroll Check Didn’t Process

If the one-time payroll check didn’t process:

Verify the payment method (direct deposit vs. paper check).
Check that the bank account is active and correctly set up in payroll settings.

11. FAQs: One-Time Payroll in QuickBooks Online

a. Can I issue a one-time payroll check without subscribing to QuickBooks Payroll?

No, the payroll feature requires an active QuickBooks Payroll subscription to issue checks.

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b. Is there a specific tax rate for bonuses?

Yes, bonuses are taxed at the supplemental wage rate, which is 22% federally as of 2024. State tax rates may