@hjw77 wrote:
My employer (the church) asked payroll to withhold my Federal income tax (calculated using salary) + Social Security and Medicare taxes (15.3%, calculated using salary + housing allowance) all under Federal income tax withheld (box 2 on W2)
I chose the option “Social Security and Medicare taxes have already been withheld” and filed my taxes. I didn’t even know that a Schedule SE was not included by TurboTax.
When I tried the Amend function in TurboTax, the only option I could find is changing my choice of the above mentioned TurboTax interview question “How should we calculate these taxes?” to “Pay self-employment tax on my wages and housing allowance.” But my question is: since I already had my SS & Medicare taxes withheld along with my Federal income tax, will this option calculate more SECA taxes than I should pay?
You did not have Social Security taxes withheld (boxes 4 and 6 of your W-2). Your employer just had 'extra' income tax withheld (Box 2 of your W-2) because that can be applied towards the self-employment tax on your tax return.
Yes, you can (and should) amend. You should select that option to pay self-employment tax on your wages and housing allowance.
It will result in you owing the correct amount of tax. Because you already filed and did not pay self-employment tax (and likely received a large refund because of the large amount of tax withheld in Box 2 of your W-2), you will likely owe quite a bit when you amend. But it will be the correct amount.
