If you incorporated your organization in California or registered your out-of-state ("foreign") nonprofit corporation in California, the Secretary of State is the agency you contracted with.
Domestic (Calif.-based) nonprofit corporations must file a Statement of Information (Form SI-100) every two years. Online filing is strongly recommended, but you may also submit it via mail.
To File the Statement of
There are 2 ways to file the Statement of Information:
(If the system does not let you file online, it means that your Statement of Information is not yet due.)
Receiving a Stamped/Filed Return Copy
When you complete the filing and payment process, you'll be given the opportunity to enter an email where a "stamped/filed" copy of the form will be sent after it's accepted.
By using their Business Search feature, once you locate your corporation you can download past filings for free.
Check your status
I recommend checking the Secretary of State's Web site every 6 months. It's the quickest way to find out if you're still in good standing with them. Click here to check your status.
(The Secretary of State's Website is particularly valuable as a "diagnostic" tool because delinquencies with other agencies will eventually show up there.)
A Common Cause of Suspension
Failure to file the Statement of Information is, in my experience, the single most common cause of corporate suspension.
To Resolve Suspension
The Secretary of State's number is 916-657-5448, but they're not always easy to reach. I usually contact the Franchise Tax Board to resolve compliance issues with the Secretary of State.
Out of State Corporations
If you're an out-of-state ("foreign") corporation registered in California, you'll need to file Form S&DC-S/N annually (go to #2 then, under that, #4 on the linked list).