Annual Filing and Governance Checklist for California Nonprofits

Robert E. Williams, Attorney at Law · Updated October 4, 2026 · 5 min read

Forming a nonprofit corporation and receiving tax-exempt status is a major milestone, but it is the beginning rather than the end of the paperwork. California nonprofits answer to several agencies, each with its own annual or periodic filing. Missing these filings can lead to penalties, loss of good standing, suspension of corporate powers, or even revocation of tax-exempt status.

This checklist summarizes the recurring filings and governance practices that keep a typical California 501(c)(3) public benefit corporation in good standing. If you are still in the formation stage, start with how to start a nonprofit in California.

Key points

Most charities file an IRS Form 990-series return every year; failing to file for three consecutive years means automatic revocation of exemption.
California requires a Franchise Tax Board Form 199 or 199N each year.
Charities registered with the Attorney General file Form RRF-1 annually.
The Statement of Information (SI-100) is filed with the Secretary of State every two years.

Federal Filings (IRS)

Form 990, 990-EZ or 990-N

Most tax-exempt organizations must file an annual information return with the IRS, due on the 15th day of the fifth month after the end of the fiscal year (May 15 for calendar-year organizations), with an automatic six-month extension available. Which form you file depends on size:

Form 990-N (e-Postcard): for organizations whose gross receipts are normally $50,000 or less.
Form 990-EZ: for organizations with gross receipts under $200,000 and total assets under $500,000.
Form 990: for larger organizations.

Churches and certain church-affiliated organizations are generally exempt from filing the 990 series. An organization that fails to file a required return for three consecutive years automatically loses its tax-exempt status, and reinstatement requires a new application.

Other federal returns

Organizations with employees must file payroll tax returns and issue Forms W-2. Those that pay independent contractors $600 or more may need to issue Forms 1099. Organizations with unrelated business income of $1,000 or more must file Form 990-T.

California Franchise Tax Board

Exempt organizations file California Form 199 (Exempt Organization Annual Information Return) or, for organizations with gross receipts normally $50,000 or less, the electronic Form 199N, due on the same schedule as the federal return. Unrelated business income is reported on Form 109. Organizations that fail to file can have their California exemption revoked and may be suspended by the Franchise Tax Board.

California Attorney General: Registry of Charities and Fundraisers

Charities registered with the Attorney General must file an Annual Registration Renewal Fee Report (Form RRF-1) each year, together with a copy of their IRS Form 990 or 990-EZ when one is filed. The RRF-1 is due four months and fifteen days after the end of the fiscal year, and the fee is based on the organization's total revenue. Organizations that do not file may become delinquent, which can prevent them from soliciting donations in California, and directors may be personally liable for late fees.

The Nonprofit Integrity Act adds further requirements. A charity with gross revenue of $2 million or more (excluding certain government grants) must have an annual audit performed by an independent CPA and make it available to the public, and it must have an audit committee (Government Code section 12586). All charities must review and approve the compensation of the president or chief executive officer and the chief financial officer to ensure it is just and reasonable.

California Secretary of State

Every two years, during the filing period based on the original month of incorporation, the corporation must file a Statement of Information (Form SI-100) updating its officers, agent for service of process and addresses. Late filing can result in penalties and, eventually, suspension. File an updated statement whenever officers or addresses change.

Other Recurring Obligations

Property tax welfare exemption: organizations that own or lease property claimed as exempt file annual claims with the county assessor.
Raffles: eligible organizations that conduct raffles must register with the Attorney General before the raffle and file a report afterward.
Local business licenses and permits: renew as required by your city or county.
Payroll and employment: state payroll filings with the Employment Development Department, workers' compensation insurance and posting requirements.
Insurance: review general liability and directors and officers coverage each year.

Governance Practices That Protect the Organization

Good governance is not only a legal requirement; it is what donors, grantmakers and regulators look for.

Regular board meetings with minutes. Record attendance, decisions and the reasons for important actions.
Conflict of interest policy. Directors should disclose conflicts annually and abstain from related votes. California law restricts self-dealing transactions between a public benefit corporation and its directors (Corporations Code section 5233).
Independent board. No more than 49% of directors may be "interested persons" (Corporations Code section 5227).
Financial oversight. The board should review financial statements regularly and approve an annual budget.
Donor acknowledgments. Provide written acknowledgments for gifts of $250 or more, and quid pro quo disclosures for payments over $75 that are partly a gift.
Restricted gifts. Track donations given for specific purposes and use them only for those purposes.
Public disclosure. Make your exemption application and three most recent Form 990s available to anyone who requests them.

A Sample Annual Calendar (Calendar-Year Organization)

January: issue Forms W-2 and 1099; review conflict of interest disclosures.
May 15: IRS Form 990-series, FTB Form 199 or 199N, and Attorney General Form RRF-1 due (or extend).
Every two years: Statement of Information during the filing window for your incorporation month.
Quarterly: payroll tax filings; board review of financial statements.
Year-end: approve next year's budget; confirm officer elections and review executive compensation.

What If You Have Fallen Behind?

Many small organizations discover missed filings years later, often when a bank or grantmaker asks for proof of good standing. Most problems can be corrected. The usual steps are to check status with each agency (the IRS Tax Exempt Organization Search, the Attorney General's Registry Search, the Franchise Tax Board and the Secretary of State's business search), file the missing returns, pay any penalties, and request reinstatement where necessary. Acting promptly limits penalties and protects directors.

Conclusion

Keeping a California nonprofit in good standing comes down to a few recurring filings and steady governance habits: the annual IRS 990-series return, the FTB Form 199, the Attorney General's RRF-1, the biennial Statement of Information, and regular, well-documented board oversight. Put the deadlines on a shared calendar, assign responsibility to a specific officer, and review compliance at least once a year. Doing so protects the mission, the donors who support it and the volunteers who serve it.

Questions About Your Own Plan?

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This article provides general information about California and federal law as of October 4, 2026. It is not legal advice and does not create an attorney–client relationship.