In 1791, due to the severe flooding which characterized the pueblo, San Jose's settlement was moved approximately a mile south, centered on the Pueblo Plaza (modern-day Plaza de César Chávez).

San Jose became part of the First Mexican Empire in 1821, after Mexico's War of Independence was won against the Spanish Crown. Just a few decades later, the territory was ceded to the United States following the American Conquest of California during the Mexican-American War (1846-1848).

With California's Admission to the Union on September 9, 1850, San Jose became the state's first capital. Legislators met in the city from 1850 to 1851. Although the first capitol building no longer exists, the Plaza de César Chávez, which now lies on the site, has two historical markers indicating where California's state legislature first met.

There are four distinct valleys in the city of San Jose: Almaden Valley, situated on the southwest fringe of the city; Evergreen Valley to the southeast; Santa Clara Valley, which includes the flat, main urban expanse of the South Bay; and the rural Coyote Valley, to the city's extreme southern fringe.

The large concentration of high-technology engineering, computer, and microprocessor companies around San Jose has led the area to be known as Silicon Valley and earned the city the nickname "Capital of Silicon Valley".

The San Jose Sharks were founded in 1991 and were the first NHL franchise based in the San Francisco Bay Area since the California Golden Seals relocated to Cleveland in 1976.

The highest temperature ever recorded in San Jose was 109 °F (42.8 °C) on June 14, 2000; the lowest was 19 °F (-7.2 °C) on December 22-23, 1990.

Because of the proximity to Lick Observatory atop Mount Hamilton, San Jose has taken steps to reduce light pollution, including replacing all street lamps and outdoor lighting in private developments with low pressure sodium lamps. To recognize the city's efforts, the asteroid 6216 San Jose was named after the city.