I'm here to share some insights on how QBO calculates payroll taxes
There are possible reasons why your federal taxes aren't calculating properly. It could be that the employee's total annual salary exceeds the wage base limit or the gross wages of the last payroll are too low.
Take note that tax calculations are derived from the payroll data and transactions you entered. The program calculate the federal withholding based on these factors:
Taxable wages
Number of allowances/dependents
Pay frequency
Filing status
You'll also want to revisit your employees’ profiles to check if they are set up correctly. Additionally, I suggest checking the Tax Withholding Estimator and IRS Pub 15 for FIT withholding tables. For the state withholding table, you can check your state agency's calculation method.
Lastly, here's an article that you can read to help track where your business stands in terms of payroll and employee expenses: Run payroll reports.
Do you have any other questions in mind? Feel free to leave them below and I'll get back to you. Have a great rest of the day.