California’s nonprofit annual filings, explained: which agency gets what, and when

Why four

Federal tax exemption and California charitable registration are different things, granted by different bodies, for different reasons. The IRS decides whether you are exempt from federal income tax. The Franchise Tax Board decides the same question for California. The Attorney General supervises charitable assets and fundraising on behalf of the public. The Secretary of State keeps the corporate record current.

None of them talks to the others on your behalf. A filing made with one does not satisfy another. This is the single most common gap we see in small nonprofit compliance, and it is almost never deliberate. It is simply that nobody told the board there were four.

1. The IRS

Every exempt organization files an annual return or notice in the 990 series. Which one depends on size. Organizations with gross receipts normally $50,000 or less file Form 990-N, the electronic notice. Larger organizations file Form 990-EZ or the full Form 990. Private foundations file Form 990-PF regardless of size.

The deadline is the 15th day of the fifth month after the accounting period closes. May 15 for a calendar-year organization. Form 8868 buys a six-month extension for Form 990 and Form 990-EZ, but it does nothing for Form 990-N, which cannot be extended.

Three consecutive missed years revokes exemption automatically under Internal Revenue Code section 6033(j). We cover that rule and the routes back in our piece on Form 990-N and automatic revocation.

2. The Franchise Tax Board

California’s version mirrors the federal structure. Organizations with gross receipts normally $50,000 or less file FTB 199N, the California e-Postcard. Everyone else files Form 199, the California Exempt Organization Annual Information Return.

Two details are worth knowing.

First, the filing fee is gone. California eliminated the Form 199 filing fee for taxable years beginning on or after January 1, 2021. Older guidance still circulating online refers to a $10 fee. It no longer applies.

Second, the extension is automatic. California grants exempt organizations a six-month extension to file Form 199 without requiring any form or request, provided the organization is in good standing. You do not file anything to claim it.

The late-filing penalty for Form 199 is $5 per month, capped at $40. Small, but it is a signal that a filing was missed, and missed filings accumulate into suspension.

3. The Attorney General’s Registry of Charities and Fundraisers

This is the agency most small boards have never heard of, and it is the one with the most moving parts.

A charity holding assets in California registers with the Registry using Form CT-1 within 30 days of first receiving charitable assets. The initial registration fee is $50.

After that, the annual filing is Form RRF-1, the Annual Registration Renewal Fee Report. It is due four months and fifteen days after the close of the fiscal year. For a calendar-year organization that is May 15, which happens to match the IRS deadline, but the alignment is a coincidence of the calendar rather than a rule, and it breaks for any organization on a non-calendar fiscal year.

What you attach to the RRF-1 depends on which return you file with the IRS. An organization that is not required to file, and does not file, Form 990 or 990-EZ files Form CT-TR-1, the Annual Treasurer’s Report, alongside the RRF-1. An organization that files Form 990, 990-EZ, or 990-PF attaches a copy of that return instead. The revenue figure behind this is $50,000 of total revenue, which is the point at which the IRS filing requirement changes. Private foundations are the exception in both directions: they file Form 990-PF whatever their size, and they never file CT-TR-1.

4. The Secretary of State

A California nonprofit corporation files a Statement of Information, Form SI-100. For nonprofits this is biennial, not annual, and the filing period is tied to the anniversary month of incorporation rather than to the fiscal year.

The fee is $20. Filing late carries a $50 penalty, and continued failure to file can lead to suspension or forfeiture of corporate status. Suspension is worse than it sounds: a suspended corporation cannot legally do business, cannot defend a lawsuit, and cannot easily be revived without clearing every outstanding filing.

The calendar, in one place

Change the fiscal year end and three of those four move together while the fourth stays where it is. A June 30 year end shifts the IRS, FTB, and Attorney General deadlines to November 15 and leaves the SI-100 exactly where it was.

What goes wrong, and what prevents it

The pattern is consistent. A board files the 990 because the accountant asks about it, and the other three drift. Registration with the Attorney General lapses, which shows up as a delinquent status on a public database that grantmakers search. The SI-100 is missed twice, and the corporation is suspended. None of it was intentional.

What prevents it is unglamorous: one calendar, held by the organization rather than by whoever happens to be treasurer, with all four agencies on it and a reminder set 45 days ahead of each deadline. Confirm your fiscal year end in writing, because it drives three of the four dates. And check your status on the Registry search tool once a year, the way you would check a credit report.

Common questions

Does filing with the IRS satisfy California's requirements?

No. Federal and California exemption are administered separately, and the Attorney General's Registry of Charities and Fundraisers and the Secretary of State have their own filings. A California charitable nonprofit generally files with all four agencies.

Is there still a fee to file FTB Form 199?

No. California eliminated the Form 199 filing fee for taxable years beginning on or after January 1, 2021. Guidance referring to a $10 fee is out of date.

When is Form RRF-1 due?

Four months and fifteen days after the close of the organization's fiscal year. For a calendar-year organization that is May 15.

When does a California nonprofit need Form CT-TR-1?

Form CT-TR-1, the Annual Treasurer's Report, is filed with the RRF-1 by organizations with total revenue under $50,000. Organizations at or above that level attach a copy of the IRS Form 990, 990-EZ, or 990-PF instead.

How often is Form SI-100 filed?

Every two years. The filing period is tied to the anniversary month of incorporation, not the fiscal year. The fee is $20 and late filing carries a $50 penalty.

What revenue level triggers a required audit in California?

Under California Government Code section 12586(e), gross revenue of $2 million or more in a fiscal year requires audited financial statements prepared by an independent certified public accountant. Grants from and contracts for services with government entities are left out of that count only where the government entity requires an accounting of the funds received.