Following the Mexican secularization of 1833, the town was briefly known as San Juan de Castro and eventually incorporated in 1896.

Prior to the arrival of Europeans, the area around San Juan Bautista was populated by the Mutsun, a tribe of the Ohlone Nation of Indigenous Californians.

The Mutsuns lived in villages in the area around San Juan Bautista, in settlements composed of thatched huts made of willow and native grasses.

Lasuén chose the site because of the area's fertile cropland, steady water supply, and sizable Indian population.

From San Juan Bautista, Castro ordered the army against potential foreign incursions.

He kept especially close watch over the movements of John C. Frémont, an American military officer who had been let into California to conduct a survey of the interior.

Though given explicit instructions to stay away from coastal settlements, Frémont soon broke the agreement by taking his team to Monterey, a potential military target.

In June 1904, early aviation pioneer John J. Montgomery made a series of successful test flights using his tandem-wing glider in San Juan.

This was a prototype to his 1905 gliders that were used to make the first successful high-altitude flights in heavier-than-air flying machines in the world.

In 1971, Luis Valdez moved El Teatro Campesino, one of the most important cultural institutions of the Chicano Movement, to San Juan.

According to the United States Census Bureau, the city has a total area of 0.7 square miles (1.8 km2), 99.94% of it land and 0.06% of it water.

San Juan is largely an agricultural community, though the town has a strong tourist industry, owing to its historic and cultural sites.

Earthbound Farm, based in San Juan, is the largest producer of organic salads in the United States.

[14] CMAP TV – Community Media Access Partnership operates Channels 17, 18, 19 & 20 on Charter/Spectrum Cable as well as streaming online, offering public access and educational programming to Gilroy and San Benito County as well as covering live civic meetings, including the City of San Juan Bautista.

The location was used for scenes in the Alfred Hitchcock film Vertigo, though the church tower, which had been demolished years earlier by fire, was added by special effects.