After earthquake damage and years of neglect, this second mission fell into disrepair, and much of it, though not all, was removed to accommodate the construction of the Holy Cross Church in 1889.

This adobe building served as housing for Indigenous families who, after being converted to Catholicism, lived and worked at the Mission.

It is the oldest surviving structure in Santa Cruz County and the best preserved Native American residence at any of the Alta California missions.

The outpost was originally established near the Uypi village of Aulintak, located near the mouth of the San Lorenzo River, on August 28, 1791.

[5] In 1797, the secular pueblo (town) of Branciforte was founded across the San Lorenzo River to the east of Mission Santa Cruz.

[12] In 1818, the Mission received advance warning of an attack by the Argentine corsair (simply a pirate, from the Spanish point of view) Hipólito Bouchard and was evacuated.

[13] The citizens of Branciforte, several of whom were retired soldiers, were asked to protect the Mission's valuables; instead, they were later accused (by the priests) of stealing.

[15] In 1889, the current Gothic Revival-style Holy Cross Church was built over (in the same orientation) part of the original sanctuary and cemetery.

In recent years, a group of local volunteers worked to restore the old cemetery, and to identify the mission gravesite and those whose remains were moved there.

Since there were no surviving photographs or drawings of the original structure, design of the replica chapel was adapted from an 1876 (19 years after the collapse of the building's front half) painting by the French painter Léon Trousset.

The concrete construction was done by parishioner Tranquilino Costella, an Italian immigrant, whose contractor stamp is still seen in the sidewalk in front of the mission.

The small replica chapel is mainly used for private services, daily Masses (M-F), and Morning Prayer on Saturday.

[7] The stone foundations of an unidentified adobe on the east edge of Mission Hill in Santa Cruz was first discovered in 1978.

Artifacts found were a diverse collection of Spanish Mission Era/ Mexican Republic materials including glass beads, Majolica ceramic fragments and phoenix buttons.

[28][29] These findings suggest that the structure was used to house the neophyte community of Yokuts and Ohlone families living at the Mission in the 1820s and 1830s.