{"question": "best payroll software for nonprofits", "category": "payroll-software", "category_name": "payroll software", "audience": "nonprofits", "audience_name": "nonprofits", "engine": "Claude (Anthropic) with web search", "model": "claude-opus-5", "asked_at": "2026-10-25T23:20:40Z", "permalink": "https://bikoosh.com/answers/s/payroll-software-nonprofits-2026-10-25", "question_page": "https://bikoosh.com/answers/q/payroll-software/nonprofits", "brands_named": [{"position": 1, "brand": "OnPay", "label": "recommended"}, {"position": 2, "brand": "Gusto", "label": "recommended"}, {"position": 3, "brand": "Aplos", "label": "recommended"}, {"position": 4, "brand": "MonkeyPod", "label": "recommended"}, {"position": 5, "brand": "QuickBooks", "label": "recommended"}, {"position": 6, "brand": "Sage Intacct", "label": "recommended"}, {"position": 7, "brand": "Intacct", "label": "recommended"}, {"position": 8, "brand": "Paylocity", "label": "recommended"}, {"position": 9, "brand": "Paycor", "label": "recommended"}, {"position": 10, "brand": "Paychex", "label": "recommended"}, {"position": 11, "brand": "SurePayroll", "label": "recommended"}, {"position": 12, "brand": "Netchex", "label": "recommended"}], "sources_cited": [{"url": "https://onpay.com/payroll-software/nonprofit-payroll/", "domain": "onpay.com", "source_type": "vendor"}, {"url": "https://www.techrepublic.com/article/non-profit-payroll-software/", "domain": "techrepublic.com", "source_type": "other"}, {"url": "https://gusto.com/resources/best-payroll-solutions-for-non-profits", "domain": "gusto.com", "source_type": "vendor"}, {"url": "https://sparkrock.com/knowledge-base/blog/payroll-software-for-nonprofits-simplify-fund-accounting-and-reduce-overhead/", "domain": "sparkrock.com", "source_type": "other"}, {"url": "https://www.paylocity.com/why-paylocity/compare/lists/payroll-software-for-nonprofits/", "domain": "paylocity.com", "source_type": "vendor"}, {"url": "https://www.paycor.com/resource-center/articles/nonprofit-payroll-complete-guide/", "domain": "paycor.com", "source_type": "vendor"}, {"url": "https://netchex.com/blog/payroll-for-nonprofits-fica-exemptions-minister-pay-and-common-mistakes/", "domain": "netchex.com", "source_type": "vendor"}], "answer_text": "Here's what I'd actually recommend, roughly in order:\n\n**1. OnPay - the default pick for most small-to-mid nonprofits.** One flat plan ($49/mo + $6 per person), unlimited pay runs, tax filing in all 50 states, and it's the one provider that advertises a real **50% discount for 501(c)(3) orgs**. It also handles the nonprofit-specific tax quirks natively: FUTA exemption at the account level, clergy/minister pay (no FICA withheld or matched), housing allowance, and 403(b) deductions. If you're a church, synagogue, or any org with ministers on payroll, this is where I'd start. ([onpay.com](https://onpay.com/payroll-software/nonprofit-payroll/), [techrepublic.com](https://www.techrepublic.com/article/non-profit-payroll-software/))\n\n**2. Gusto - best if ease of use and your accountant's workflow matter most.** $49/mo + $6/person on Simple, scaling to Plus ($80 + $12) for time tracking and Premium ($180 + $22) for HR support. No flat nonprofit discount, but it integrates with the fund-accounting tools nonprofits actually use - **Aplos** and **MonkeyPod**, plus QuickBooks. Best onboarding experience of the bunch; good for a 5-50 person org without a dedicated finance staffer. ([gusto.com](", "answer_truncated": true, "measurement": "One answer from one engine on one date. Not a ranking and not a claim about the world; brands the engine did not name are not recorded.", "limitation": "Coverage: Claude (Anthropic) with web search. Other engines not included.", "alerts": {"name": "Answer Watch Pro", "price_usd": 79, "period": "month", "gets": "daily change alerts for up to 5 brands in what one AI answer engine says, history, CSV export. Coverage: Claude (Anthropic) with web search. Other engines not included", "url": "https://bikoosh.com/answers"}}