Since I don’t know whether an employee will make less than $100 until they stop working, I will have cut paychecks with taxes withheld. What do I do with the money withheld and sent into the government using a 941? Do I have to back it out of the next 941 and reimburse the employee for the amount withheld?
I run into this situation regularly. We hire high school students as part-time janitors. Sometimes the work schedule doesn’t fit, and they quit after having worked only a few days. Similarly, we hire women as paid babysitters. Again, some decide it’s not the right job and quit after earning only a few hours at minimum wage.
However, if the organization, including churches, withheld FICA and/or Medicare taxes from the employee, the organization must issue the employee a Form W-2 reflecting the payment of those taxes.
To prevent an administrative nightmare over such a few dollars, I recommend that churches withhold FICA and Medicare taxes from all employees. Even if you’re not sure whether they’ll earn more than $100 by year’s end, you’ll save yourself lots of time compared to the minimal amount of money your church may save in payroll taxes by exempting them from FICA and Medicare taxes.