Good day, @tom260. I hope you're doing well. I have a few ideas based on what you've shared, but I need to grasp the situation more accurately to offer an appropriate solution.
First, could you please confirm whether you are currently in the process of running payroll or if these paychecks have already been processed? Knowing the status will help us provide more targeted assistance. Moreover, if you could specify whether this issue is occurring for all employees or just specific ones, that would be extremely helpful.
For better understanding of how QuickBooks calculates payroll taxes, I'd like to share some important insights. QuickBooks Online Payroll automatically calculates taxes based on several factors like the employee's W-4, pay frequency, and gross wages, using the percentage method. This means FIT amounts may fluctuate during the year if additional payments such as bonuses are given. Other taxes like Social Security, Medicare, and state-specific taxes are set by agencies and updated automatically within QuickBooks. For more detailed information, you can refer to the QuickBooks article: Understand how your payroll taxes are calculated.
In the meantime, I suggest checking your employee's profiles, especially their W-4 information, to ensure that the data in QuickBooks corresponds correctly with what your employee has provided. Errors in W-4 data can lead to inaccurate tax calculations.
- Navigate to Payroll, then Employees.
- Select the employee you wish to review.
- Click on Tax withholding, then choose Edit.
- In the Federal Withholding section, confirm the details from your employee’s W-4.
- Hit Save when done.


You might also want to review these resources for state and local taxes:
I recommend checking this material: Pay and file payroll taxes and forms electronically in QuickBooks Online Payroll. It provides a step-by-step guide on managing and submitting your payroll taxes and forms efficiently and electronically through QuickBooks. It covers everything from setting up electronic services to submitting forms directly through the platform.
Moreover, to elevate your payroll management experience, Explore QuickBooks Payroll. It will show you everything you can do with QuickBooks Payroll, from the simple to the more advanced features. Learning all these can really make your payroll tasks easier and more efficient.
I'll keep this thread open for your confirmation and additional details, allowing me to further assist you in resolving this issue. Looking forward to hearing from you soon. Have a great day!