Step 1
Funding sources
Licensed Enrolled Agents - Nationwide Virtual Service
Nonprofit accounting services for organizations
A missed Form 990 deadline can cost a nonprofit its exempt status after three consecutive years. ProTax USA is an EA firm handling annual filing preparation, financial statement reviews, and internal controls that satisfy your board and your grantors. A dedicated bookkeeper and accountant stay on your account year-round. Compliance stays current, not catch-up. Book online or call now.
What You Get
What does our nonprofit financial management service actually cover?
Nonprofit accounting runs on different rules than for-profit bookkeeping. ProTax USA sets up fund accounting that separates donor-restricted funds from general operating funds, tracks functional expense allocation across program, management, and fundraising, and prepares the required annual return, including the unrelated business income filing when it applies. A non-profit organization that mixes restricted and unrestricted funds in one ledger creates problems at review time and at grant renewal time. Compliance work doesn't stop at the federal return. ProTax USA reviews internal controls around cash handling and donor records, checks whether that federal audit requirement applies under OMB Uniform Guidance for organizations spending over $750,000 in federal funds, and keeps exemption documentation current. We also help boards build an annual budget that lines up with the fund structure, so spending stays on track between reviews. Nonprofit boards ask for financials they can actually read; we build that financial reporting too as part of our broader bookkeeping services.
How It Works
How does ProTax USA start working with a new nonprofit client?
The first call runs about 30 minutes and covers your nonprofit's current bookkeeping setup, funding sources, and whether you've had an outside review before. Most nonprofits come in with QuickBooks set up like a for-profit business, with no fund accounting structure at all. ProTax USA rebuilds the chart of accounts around program, management, and fundraising categories, sets up donor restriction tracking, and prepares the annual return well ahead of the deadline instead of scrambling in the final week. Your staff doesn't need to become accounting experts overnight; we handle the setup. If your nonprofit needs one for a grantor or state requirement, we prepare the schedules reviewers ask for first, so the review process moves faster and costs less.
Step 2
Chart rebuild
Step 3
Restriction tracking
Step 4
990 preparation
Step 5
Audit schedules
Why It Matters
Why do nonprofit boards choose ProTax USA?
Most accounting firms treat a nonprofit like a small business that doesn't pay income tax. That misses fund accounting, functional expense reporting, and the extra review requirements that come with federal grant funding. As an EA firm, ProTax USA works with nonprofit organizations specifically, from small groups filing the simplified annual return to larger nonprofits managing multiple grant cycles and employee benefit plans. Executive directors and board members need financial statements that hold up in front of grantors, not just documents that clear an IRS submission. ProTax USA's Enrolled Agents build reporting that shows exactly how restricted funds were used, flags any unrelated business income before it becomes a problem, and keeps your exemption documentation ready for the next grant application. That's real advisory services built for the accounting needs of the nonprofit sector, ProTax USA acts as an advisor to your board, not a generic small business package.
Generic firm
Nonprofit CPA
Fund accounting
Often missed
Built in
Grant reports
Basic
Board-ready
UBI risk
Reactive
Flagged
Audit prep
Late
Prepared
Pricing Clarity
How much does this cost for nonprofits?
ProTax USA's services for nonprofits start at $300/month for a small not-for-profit filing the simplified annual return with straightforward bookkeeping. Our Enrolled Agents review organizations managing multiple grants, restricted funds, or an outside review, typically running $600 to $1,500/month depending on grant volume and review scope. That single audit under OMB Uniform Guidance is quoted separately as a project fee, based on the number of federal award programs involved, and ongoing tax work is included in every monthly plan. Many boards find it more cost-effective to outsource this work entirely rather than train staff internally. ProTax USA reviews your organization's books during a free consultation before quoting a real number, not a flat rate off a website. Book that call to see where your organization lands.
Small nonprofit
Multiple grants
Federal audit threshold
Single audit
Related ProTax USA Services
Explore more ways we can help
Small business accountant for small business owners
ProTax USA offers small business accounting services, bookkeeping, and full-service tax solutions. Your trusted partner for business success.
Small business tax preparation services
Expert tax preparation for your small business. From tax filing to comprehensive services, get the preparation you need for your business taxes.
Small business tax planning services
Maximize savings with expert small business EA tax support. Our business tax planning services offer comprehensive solutions for your tax services needs.
Small business bookkeeping and tax services
Expert bookkeeping & tax services for small businesses. Streamline your finances with tailored bookkeeping services, tax filing, and business taxes.
Small company payroll services
ProTax USA handles small business payroll, EFTPS deposits, quarterly 941 filings, and year-end W-2 preparation. Flat monthly pricing, no surprise fees. Book a call today.
Sales tax compliance services for small businesses
Sales tax compliance, filing, and consulting for small businesses. ProTax USA tracks your nexus, files on time, and handles back taxes through VDA programs. Flat monthly pricing.
FAQ
Common questions about accounting services for nonprofits
Tax
Scope
IRS
Tax Does a nonprofit organization need professional help if it doesn't pay income tax?
Yes. A firm like ProTax USA handles annual return preparation, fund accounting, and review support, none of which relate to income tax. Nonprofit tax rules and non-profit tax exposure aren't the same as income tax exposure. ProTax USA also monitors unrelated business income, which can trigger a tax bill even for a tax-exempt organization.
Scope What happens if a nonprofit misses its Form 990 deadline?
Missing the annual return for three consecutive years results in automatic revocation of exempt status. ProTax USA tracks deadlines and prepares tax filings well before the due date so this never becomes an issue.
Scope When does an organization need an outside financial review?
Many states require an audit once a nonprofit crosses a revenue threshold, often around $500,000 to $750,000, and most grantors require one regardless. ProTax USA prepares the schedules and reconciliations a reviewer needs before the process begins.
IRS What is a single audit and does our organization need one?
It applies to nonprofits spending $750,000 or more in federal awards in a fiscal year, under OMB Uniform Guidance. ProTax USA reviews your federal funding to confirm whether the threshold applies and prepares the required schedule of expenditures.
Tax How does ProTax USA handle donor-restricted funds?
ProTax USA sets up fund accounting that tracks each donor restriction separately from general operating funds, so nonprofit financial statements show exactly how restricted money was spent. This keeps your organization compliant with both donor agreements and review standards.
Tax Can a nonprofit lose its tax-exempt status over accounting mistakes?
Yes, most commonly from missed annual returns, unreported unrelated business income, or private benefit issues found during a review. ProTax USA reviews compliance annually so small accounting errors don't turn into a status revocation.