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Federal income taxes are calculated based on the employee's W4 information and gross wages, mattheikkila.
You can go to the employee's set up to check if there's something that's causing the miscalculation. Here's how:
I would also recommend contacting our Payroll Support Team. They can help you review the amounts to check what's causing the issue. Here's how:
Please reply below if you have follow-up or any other questions. We're always here to guide and assist you while working in QuickBooks.