St Peter's church was built in 1857 on land purchased from Richard Connor for £5. The church was built by Michael Cook, John Clarke gave stone and other building materials, and the church was furnished by parishioner Patrick Leonard. The church opened on 1 January 1858.

Behind the church is a cemetery, in which the earliest recorded burial is dated to 1869. Two notable pioneers buried in the cemetery are John and Catherine Clarke. John came to South Australia in 1836, Catherine in 1838, they married in 1840 and established their home at Wattle Flat.

This church was attended by the Sisters of St Joseph, whose school was located in Yankalilla from 1867 to 1874. It is believed the Mary MacKillop, the co-founder of the order and first professed sister, visited Yankalilla in 1869. In 2010 a plaque was installed in the grounds of the church, to mark the canonisation of Mary MacKillop.

Photograph 2020 by Karen Toleman.