On January 12, 1777, Franciscan missionaries erected a cross at the Ohlone village of So-co-is-u-ka, a name meaning "Laurelwood," on the banks of the Guadalupe River. They called the outpost La Misión Santa Clara de Thamien, after the Tamien people who lived there. It was the eighth mission established in California. Almost immediately, the river conspired against it. Floods washed away the early structures and forced relocation to higher ground. A second site, then a third, then a fourth followed over the decades. The current location dates to 1825, making it the mission's fifth permanent home. Native American burial sites discovered near the third site, west of the modern Caltrain tracks, testify to the Ohlone community that lived and died under the mission system.

The mission's early years were marked by conflict with the nearby Pueblo de San José over land and water rights. Two hundred Native Americans built a road called the Alameda to connect the two settlements and ease the tension. On Sundays, residents of San Jose walked this road to attend Mass at the mission, a practice that continued until St. Joseph's Church was completed in 1803. By that year, the mission reported a Native American population of 1,271 and an astonishing agricultural operation: 10,000 cattle, 9,500 sheep, 730 horses, and roughly 3,000 fanegas of grain. It was a self-sustaining world unto itself, one that the Mexican secularization act of 1833 would soon dismantle.

After secularization, Mexico subdivided and sold the mission's land, often to government officials, with half nominally allocated to Native Americans. Most California missions fell into ruin. Santa Clara was different. Its buildings continued serving as a parish church, and in 1851, Santa Clara College was founded on the grounds. It became the first institution of higher learning in Alta California and eventually grew into Santa Clara University, making this the only California mission situated on a university campus. The mission is the namesake of the city, the county, and the university that envelops it.

The mission kept changing its skin. In 1861, workers attached a new wooden facade with twin bell towers over the old adobe front. In 1885, they widened the interior by tearing out the original adobe nave walls to fit more worshippers. Then, in 1925, fire consumed the entire structure, including the surrounding wall. The parish relocated to Saint Clare Parish west of campus. Four years later, a rebuilt and restored mission was consecrated in 1929, assuming its modern role as the university chapel. The bell tower holds three bells. One was a gift from King Carlos IV of Spain, but fire claimed it. King Alfonso XIII sent a replacement, which now sits in the De Saisset Museum on campus. The mission cemetery on nearby Lincoln Street, founded alongside the mission in 1777, remains in use today.

Walk the campus of Santa Clara University today and the mission sits at the center, an adobe-colored anchor surrounded by modern academic buildings and the constant motion of students. The De Saisset Museum houses the replacement bell and mission artifacts. Visitors can enter the chapel daily. It is a strange and affecting thing to stand in a space founded when the American Revolution was barely underway, rebuilt six times, and now functioning as the spiritual center of a university in the heart of Silicon Valley. The 8:30 bells still sound, a recording now rather than bronze striking bronze, but faithful to a king's request made before the United States existed.