Nonprofits & Religious Organizations: How to Calculate Your Payroll Costs (2026)

Managed payroll by headcount for a nonprofit

10 employees: $450 a month, $5,400 a year; 25 employees: $1,125 a month, $13,500 a year; 50 employees: $2,250 a month, $27,000 a year; 100 employees: $4,500 a month, $54,000 a year. Every row is $45 per employee per month, all-inclusive, inside the payroll software you already use, with no monthly minimum, so the per-employee cost is the same at 10 as at 100. Nothing in the nonprofit setup, grant-funded payroll allocation, clergy housing allowance, FUTA exemptions and volunteer to employee transitions, is billed as an add-on.

The employer-side tax that rides on every nonprofit wage

At the May 2025 national median for social and community service managers, $80,390 a year or about $39 an hour, the employer share of Social Security and Medicare is $6,150 per employee per year and FUTA is $42 after the state credit, before state unemployment at the assigned rate. Those costs are the same whoever runs payroll; the calculator question is only who does the work and who carries the error.

An organization exempt from income tax under section 501(c)(3) is also exempt from FUTA, and the exemption cannot be waived. Nonprofits that are not section 501(c)(3) organizations are not exempt and report FUTA on Form 940.

The in-house line in the calculation

BLS OEWS May 2025: payroll and timekeeping clerks, national median $58,260, mean $59,630. Add roughly 30 percent for benefits and employer taxes, about $75,738, before the software that person runs, and set it against the headcount rows above. Managed payroll stays under that loaded figure until about 140 employees.