Following the Battle of Monterey, the Americans held northern California but General José María Castro and Governor Pío Pico planned resistance in the south around the Los Angeles area. Commodore Robert F. Stockton arrived at Monterey Bay aboard the Congress on July 15 and took over command from John D. Sloat. Stockton accepted the Bear Flag revolutionaries, under the command of Major John C. Frémont, as the California Battalion. Stockton then garrisoned Sonoma, San Juan Bautista, Santa Clara, and Sutter's Fort. Stockton's plan for dealing with Castro was to have Commander Samuel Francis Du Pont carry Fremont's men in the Cyane to San Diego to block any movement southwards, while Stockton would land a force at San Pedro which would move overland against Castro. Fremont arrived at San Diego on July 29 and reached San Pedro on August 6 aboard the Congress.

On August 13, 1846, Stockton led his column into town, followed by Fremont's force a half-hour later. On August 14, the remnants of the Californio army surrendered. On September 23, twenty men under the command of Cerbulo Varela exchanged shots with the Americans at Government House, which ignited Los Angeles. On September 24, 150 Californios, organized under José María Flores, a Mexican Officer who remained in California, at Castro's old camp at La Mesa. Gillespie's forces were effectively besieged, while Gillespie sent Juan "Flaco" Brown to Commodore Stockton for help. Gillespie's men retreated to Fort Hill on September 28, but without water, they surrendered the next day. Terms called for Gillespie's men to leave Los Angeles, which they did on September 30, 1846, and boarded the American merchant vessel Vandalia. Flores quickly cleared the remaining American forces in southern California.