Payroll & Benefits Coordination for Nonprofits

Compliance-Driven. Mission-Focused. Payroll That Works for You.

payroll and calculator close up for earnings statement

Running payroll at a nonprofit isn’t the same as running payroll in the private sector—and we treat it that way. At Non-Profit Books, we specialize in helping tax-exempt organizations streamline payroll processing, track grant-funded salaries, and stay compliant with labor and IRS regulations.

We understand the nuances that come with nonprofit payroll: split funding allocations, employee classifications across programs, special requirements for clergy or education staff, and the added complexity of managing fringe benefits. Whether you're tracking FTEs for a federal grant or reporting health insurance contributions on your Form 990, we make sure no detail gets overlooked.

Our team doesn’t just run payroll—we coordinate it with your broader financial picture. We sync payroll with your fund accounting system, ensuring wages and benefits are posted accurately to programs, grants, or restricted funds. The result? Real-time clarity on your staffing costs and full alignment with your financial reporting and budgeting processes.

In addition to processing payroll, we offer support with benefits administration, including coordination of health insurance, retirement contributions, and PTO policies. We’ll help you navigate changing compliance requirements, file the necessary payroll tax forms, and handle year-end reporting like W-2s and 1099s with precision.

At Non-Profit Books, we serve exclusively mission-driven organizations—and it shows in the care we bring to every engagement. Whether you're a small nonprofit with a part-time staff or a growing organization managing multiple programs, we can help you build a payroll system that’s clean, compliant, and stress-free.

Let us take payroll off your plate—so your team can focus on what really matters: your mission.

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Non-Profit Accounting is not a CPA firm and does not provide assurance services.