A series of earthquakes in 1857 destroyed the mission. The mission was put up for sale, but no one wanted to buy it. In 1858 a wood frame church was built on the old mission property. In 1889 the current Gothic style Holy Cross Church was built on the original adobe mission site. There is nothing left of the original mission except for a row of buildings which at one time housed local Yokut and Ohlone Indian families. In 1931 Gladys Sullivan Doyle proposed to build a replica of the mission; she used her own money to build a half size replica of the original church.
The Mission Santa Cruz is a museum open to visitors. The Holy Cross Church on the site of the original church is an active and busy parish. The half size chapel has weekday masses and is available for weddings and funerals.