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Run the Payroll Fee Auditor →Blog · Payroll Management · Nonprofit
Nonprofits & Religious Organizations: Payroll Software vs. Managed Payroll Service (2026)
Payroll software gives a nonprofit the fields; managed payroll gives it someone accountable for filling them correctly, which for nonprofits means grant-funded payroll allocation, clergy housing allowance and FUTA exemptions configured against the rules cited here rather than left at defaults. BEG runs nonprofit payroll for $45 per employee per month inside the payroll software you already use, all-inclusive, live in 3 to 5 business days.
What software leaves to a nonprofit to get right
Program staff and case managers classified as exempt executive, administrative, or professional employees must be paid on a salary basis of at least $684 per week ($35,568 per year). Employees below that level are owed overtime for hours over 40 in a workweek.
Nonprofit charitable organizations are not covered enterprises under the FLSA unless they run ordinary commercial activities, such as a gift shop or fee-based services, with at least $500,000 in annual sales or business done. Employees working in the charitable activities can still be covered individually if they engage in interstate commerce, such as interstate phone calls or shipping.
The honest comparison
Software at roughly $40 to $150 a month plus $5 to $12 per employee handles a single-state, all-W-2, hourly-and-salary payroll well, and the customer owns every configuration decision, every deposit and every notice. Managed payroll at $45 per employee per month, with no monthly minimum, owns the configuration, the deposits, the filings and the corrections. For nonprofits the deciding question is who documents the exemption status of program staff and case managers and who rebuilds the pay codes when the rule changes.
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.
- Program staff and case managers classified as exempt executive, administrative, or professional employees must be paid on a salary basis of at least $684 per week ($35,568 per year). Employees below that level are owed overtime for hours over 40 in a workweek. [DOL WHD, Earnings thresholds for the EAP exemption (29 CFR 541.600)]
- Nonprofit charitable organizations are not covered enterprises under the FLSA unless they run ordinary commercial activities, such as a gift shop or fee-based services, with at least $500,000 in annual sales or business done. Employees working in the charitable activities can still be covered individually if they engage in interstate commerce, such as interstate phone calls or shipping. [DOL Fact Sheet #14A]
Read the full guide to fully managed versus self-service payroll, 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 payroll software get wrong for nonprofits?
Program staff and case managers classified as exempt executive, administrative, or professional employees must be paid on a salary basis of at least $684 per week ($35,568 per year). Employees below that level are owed overtime for hours over 40 in a workweek.
When is software the right answer for a nonprofit?
A single state, all W-2, hourly and salary pay, no grant-funded payroll allocation, and under about 20 employees, where software's lower per-employee cost outweighs what a managed service adds.
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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