During the Spanish and Mexican eras in California, there were five presidios in the region: San Diego, Santa Barbara, Monterey, San Francisco, and Sonoma. Were any of these ever conquered, taken over, or destroyed? (During the Spanish and Mexican eras, that is.)
Rebels of the Bear Flag Revolt took the Sonoma Presidio in June 1846. They made it their stronghold. The revolt didn't advance much further, however Sonoma was never retaken (though efforts had been made) before the US military came in July peacefully acquiring Sonoma from the "Bears" having declared California for the United States.