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Withholding and Paying FICA Taxes FICA taxes go toward Social Security and Medicare. Your 501(c)(3) must withhold and pay these taxes from employees’ wages, with one exception: If your organization pays an employee less than $100 in any calendar year, it need not withhold FICA taxes for that employee. A 501(c)(3) must pay both the amount of FICA tax withheld from employees’ wages and the organization’s match of that amount.
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