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Run the Payroll Fee Auditor →Blog · Payroll Management · Nonprofit
Nonprofits & Religious Organizations: Managed Payroll for Mid-Size Businesses (25-100 Employees) (2026)
Managed payroll for a mid-size nonprofit, 50 to 100 employees, is where FMLA and the ACA employer mandate have attached and the question becomes whether to hire the payroll clerk BLS prices at $58,260 or pay $3,375 a month at 75 employees. BEG: $45 per employee per month inside the payroll software you already use, live in 3 to 5 days.
What attached at 50 for a nonprofit
FMLA covers a nonprofit with 50 or more employees in 20 or more workweeks, with job-protected unpaid leave and benefits continued, so leave balances, intermittent hours and benefit deductions during leave all live in payroll. The ACA applicable large employer test counts full-time equivalents from payroll hours, and once it applies the 1094-C and 1095-C filings are built from the same data every year. For nonprofits with part-time program staff the FTE count is the number to watch, not the headcount.
Hire or outsource at 75 employees
BLS OEWS May 2025 puts the national median for payroll and timekeeping clerks at $58,260, roughly $75,738 loaded, for one person who also has to know grant-funded payroll allocation, clergy housing allowance and FUTA exemptions and who is a single point of failure on every pay date. Managed payroll at 75 employees is $3,375 a month, $40,500 a year, with the ACA and FMLA mechanics inside the price. The next federal lines, WARN notice and the EEO-1 report, wait at 100.
Salaries and wages charged to federal awards must be based on records that accurately reflect the work performed and that support the distribution of an employee's pay among activities when the employee works on more than one federal award or on both federal and non-federal activities. Budget estimates alone do not qualify as support for the charges.
The rules behind this page, with sources
General information, not legal advice. Every rule below was read on the agency page linked next to it.
- Salaries and wages charged to federal awards must be based on records that accurately reflect the work performed and that support the distribution of an employee's pay among activities when the employee works on more than one federal award or on both federal and non-federal activities. Budget estimates alone do not qualify as support for the charges. [2 CFR 200.430(g)]
Read the full guide to managed payroll by company size, and the rest of the nonprofit payroll library.
Managed Payroll, Handled.
BEG manages payroll at $45 per employee per month, all-inclusive. Get an instant cost comparison for your business.
Frequently Asked Questions
What does managed payroll cost a nonprofit with 75 employees?
$3,375 a month at $45 per employee, all-inclusive, including the 1094-C and 1095-C build.
Is a mid-size nonprofit an applicable large employer?
If it averaged 50 or more full-time employees plus full-time equivalents in the prior year, yes, and the count comes from payroll hours.
What does the in-house alternative cost at this size?
$58,260 a year at the BLS OEWS May 2025 national median for a payroll and timekeeping clerk, before benefits, employer taxes and software.
What does managed payroll cost for a nonprofit?
$45 per employee per month, all-inclusive, inside the payroll software you already use, with no monthly minimum. Grant-funded payroll allocation, clergy housing allowance and FUTA exemptions are configured at setup, not billed as add-ons.
Related Resources
Anthony leads payroll solutions at Business Executive Group, a national managed payroll firm serving businesses across industries including Nonprofits & Religious Organizations. BEG manages payroll at $45 PEPM, all-inclusive, with deep expertise in compliance, multi-state filing, and industry-specific payroll requirements. Get instant pricing at beghr.com.
Authoritative source: U.S. Department of Labor: Wage and Hour Division
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