Filing Form 990-EZ costs nothing at the IRS window. The federal government charges no fee to submit the return. The real cost of filing a 990-EZ is the preparation work behind it, which typically runs $500 to $1,500 if you hire a CPA, or 15 to 50 hours of staff time if you handle it in-house. Late filing and missed deadlines can add far more on top of that, so the number worth budgeting for is not the filing itself but everything that goes into producing an accurate return on time.
What the IRS Charges
Zero. There is no government filing fee for Form 990-EZ. The return must be filed electronically, though, so you will need either IRS-approved e-filing software or a preparer who submits electronically on your behalf.1Internal Revenue Service. Instructions for Form 990-EZ Paper submissions are no longer accepted.
One quick boundary before the numbers: the 990-EZ is for organizations with gross receipts under $200,000 and total assets under $500,000 at year-end.1Internal Revenue Service. Instructions for Form 990-EZ If your gross receipts are normally $50,000 or less, you can file the far simpler Form 990-N (the e-Postcard) instead.2Internal Revenue Service. Annual Electronic Filing Requirement for Small Exempt Organizations – Form 990-N (e-Postcard) Cross either the receipts or asset threshold and you file the full Form 990. Churches, state institutions, and qualifying governmental units are exempt from filing any 990 at all.3Internal Revenue Service. Annual Exempt Organization Return: Who Must File
What a CPA Will Charge to Prepare It
Hiring a CPA or professional tax preparer is the most visible direct cost. For a straightforward organization with clean books, professional preparation fees generally fall between $500 and $1,500. The lower end applies to organizations with simple operations and well-organized records. Fees climb toward the upper end when the preparer has to reconcile poor bookkeeping, address unrelated business income, or complete additional attached schedules like Schedule O.
Location moves the price. Firms in major metropolitan areas may charge 20 to 30 percent more than comparable practices in smaller markets. Firm size and nonprofit specialization matter too. Large national accounting firms tend to charge more than small local CPA practices, though the quality gap on a return as relatively contained as the 990-EZ is not always proportional to the price difference.
A typical engagement covers preparation of the 990-EZ, required schedules, and electronic filing. Many preparers also consult on the public support test, which matters for maintaining 501(c)(3) status. If your organization needs a formal financial review or audit before the return is prepared, expect another $500 to $1,000 or more for that work. Clarify the scope before you sign anything. Surprise charges for “additional schedules” or “complexity adjustments” are a common frustration.
What It Costs to Prepare It In-House
If you skip the CPA, the money you save shows up as hours instead. Preparing the 990-EZ means compiling revenue and expense figures into specific IRS categories, including the breakdown between program services, management and general expenses, and fundraising costs.
An organization with clean, consistent bookkeeping can usually handle this in 15 to 25 hours of focused administrative work. Organizations with multiple revenue streams, complex grant reporting, or records that were not maintained consistently should plan for 35 to 50 hours. This time usually falls on an executive director or treasurer. At a fully loaded rate of $50 an hour, that is $750 to $2,500 of staff time that rarely gets tracked as a filing cost.
Then there is software. Nonprofit-focused accounting software runs $300 to $1,500 a year depending on features. Some IRS-approved e-filing platforms charge separately for the electronic submission itself. Training staff to use these tools correctly is another quiet cost. The expense categorization the 990-EZ requires is not intuitive, and miscategorized transactions can create problems later, especially if you eventually hand the work to a CPA.
Year-round record-keeping is the single most effective way to hold these costs down. Organizations that keep supporting documentation for every revenue and expense item as they go spend far less time consolidating figures at filing season.
Add-Ons That Can Raise the Bill
Form 990-T for Unrelated Business Income
Any exempt organization with $1,000 or more of gross income from a regularly conducted trade or business unrelated to its exempt purpose has to file Form 990-T and pay tax on that income. The federal tax rate on unrelated business taxable income is 21 percent. If you expect to owe $500 or more for the year, estimated tax payments are also required.4Internal Revenue Service. Unrelated Business Income Tax Preparation fees rise accordingly. Gift shops, facility rentals, and paid advertising in publications are common triggers worth checking.
State Registration and Reporting
Federal filing is only part of it. Many states require nonprofits soliciting donations from their residents to register with a state agency and file periodic financial reports. Fees range from nothing to roughly $75 per state. If you fundraise across state lines, multistate registration adds up quickly, and the professional fees to keep it all current can rival the cost of the 990-EZ itself. A few states also have added requirements when paid solicitors are used or when an organization holds assets subject to a charitable trust.5Internal Revenue Service. Charitable Solicitation – State Requirements
What Missing the Deadline Costs
The 990-EZ is due on the 15th day of the fifth month after your fiscal year ends. For calendar-year filers, that means May 15.6Internal Revenue Service. Annual Exempt Organization Return: Due Date You can file Form 8868 by the original due date for an automatic six-month extension, no approval needed, which pushes calendar-year returns to November 15.7Internal Revenue Service. Extension of Time To File Exempt Organization Returns
For returns required to be filed in 2026, the IRS penalties for late or incomplete returns are:8Internal Revenue Service. Rev. Proc. 2024-40
- Smaller organizations, meaning gross receipts of $1,309,500 or less: $25 per day the return is late, capped at the lesser of $13,000 or 5 percent of gross receipts for the year.
- Larger organizations, meaning gross receipts above $1,309,500: $130 per day, capped at $65,000.
- If the IRS sends a written demand to file and the organization still does not comply, the IRS can assess $10 per day against the individual responsible for the failure, up to $6,500.
The penalties are adjusted for inflation each year under IRC Section 6652(c).9Office of the Law Revision Counsel. 26 USC 6652 – Failure To File Certain Information Returns, Registration Statements, Etc. They apply equally to returns filed late and to returns filed on time that are incomplete or incorrect.
The Bigger Cost: Losing Exempt Status
The worst outcome is not a penalty at all. If an organization fails to file a required Form 990, 990-EZ, or 990-N for three consecutive years, the IRS automatically revokes its tax-exempt status.10Internal Revenue Service. Automatic Revocation of Exemption There is no warning letter and no appeal. Revocation takes effect on the due date of that third missed return.
Once revoked, the organization files as a taxable entity and may owe federal and state income taxes on its revenue. Donors lose the ability to claim tax deductions for contributions, which can undo fundraising quickly. Reinstatement requires a new application for exemption, usually Form 1023 or Form 1023-EZ, together with the IRS user fee and all delinquent returns. Professional fees for that process alone can run into the thousands, and the timeline is months rather than weeks. Organizations that apply within 15 months of appearing on the IRS revocation list may qualify for retroactive reinstatement; miss that window and you face a gap in exempt status that can create tax liability for the intervening period.11Internal Revenue Service. Automatic Revocation – How To Have Your Tax-Exempt Status Reinstated
The IRS revocation list is public and searchable, so donors and grant-makers can see it. That reputational effect can linger even after reinstatement is complete. Set against that, the cost of a $500 to $1,500 preparer, or a few dozen hours of staff time, is the easy part of the bill.