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Nonprofit Accountant and Form 990 Preparation

Private schools, tutoring centers, trade schools, 501(c)(3) foundations, churches, and charter schools: we prepare Form 990, manage unrelated business income, and keep your organization clean, transparent, and protected.

How we work with this industry

A nonprofit is judged on its filings in a way a business is not: the annual return is public, funders read it, and losing exempt status is far harder to undo than to avoid. Restricted and unrestricted funds have to be tracked separately, and payroll for a mixed staff and contractor team has to be right. We keep the fund accounting clean and the annual filing on time.

Fund accounting is the part that has to be right from the start. A restricted grant is a promise about how money will be used, and the books have to show that promise being kept without anyone rebuilding the year from receipts first. We set the chart of accounts up so restricted and unrestricted balances, and the programs they belong to, stay separable at any point in the year.

The other recurring work is payroll and the annual return. Schools and nonprofits usually run a mixed team, salaried staff alongside contract instructors and coaches, and the classification has to hold up. We handle the pay runs and the payroll filings, allocate expenses across program, management and fundraising as the year goes, and prepare the annual exempt organization return from books that already answer the questions it asks.

A teacher working with students in a classroom.

What We Handle for Schools and Nonprofits

The bookkeeping, payroll and filing work an exempt organization needs to stay readable to its board, its funders and the IRS.

  • Fund Accounting Set Up Properly

    A chart of accounts where net assets with and without donor restrictions, and the program each dollar belongs to, can be separated at any point without reconstructing the year.

  • Functional Expense Allocation

    Salaries, rent and overhead split across program, management and fundraising as they occur, because that split is what the full annual return asks charitable organizations to show, and what most funders ask to see.

  • Grant and Restricted Fund Reporting

    Spending tracked against each award as it happens, so a funder report is something you print rather than a project you take on.

  • The Annual Exempt Organization Return

    Whichever return your organization actually owes, from the 990-N postcard through the full Form 990 or a 990-PF, prepared on your organization's own fiscal year, from books that already carry the detail it asks for, and filed before the deadline rather than against it.

  • Staff and Instructor Payroll

    Pay runs, W-2s for employees, 1099-NEC reporting for contract instructors, and Form 941 kept on its own schedule. Exempt organizations sit outside federal unemployment tax, and Florida reemployment tax turns on how many people you employ and for how many weeks, so we confirm where your organization actually lands instead of filing returns it does not owe.

  • Tuition, Program Revenue and Gifts

    Fees, enrollment deposits and contributions recorded distinctly, including the pieces that arrive in the same deposit, so neither one disappears inside the other.

Common Problems

Where Nonprofit and School Books Go Wrong

Four failures that surface at the worst moment, usually during a funder request or the annual filing.

  • Restricted Money Spent as General Funds

    Cash sitting in one account does not make it unrestricted. Spending a restricted award on operations is a problem with the donor well before it is ever a problem with the books.

  • Every Expense in One Bucket

    Without a functional split made through the year, program, management and fundraising get estimated at filing time. An estimate is exactly what a careful funder will ask about.

  • Instructors Paid as Contractors by Default

    Classification follows how the work is directed and scheduled, not which check is easier to write. Getting it wrong reaches back through payroll filings that were already due.

  • Unrelated Business Income Nobody Flagged

    Advertising, a shop, or a regular activity outside the mission can carry a return of its own once it clears a low gross-income floor. Rent from your own building usually does not, though a debt-financed property or a rental bundled with services can change that. Manageable when identified early, awkward when found during a review.

Questions we hear in this industry

Straight answers, from an Enrolled Agent.

Need help in your industry?

Talk to us about how we can help you stay compliant and grow.