The original Mill Bay Church, built in 1897 and opened in 1898, functioned as a Methodist Church until 1925 and as a United Church for many years thereafter. The church is a one-story wood framed building supported on original timber foundation posts on grade over a crawlspace in which remedial work has occurred in the past. The church site was donated by the Sylvan United Church to the CVRD in 2007. The CVRD now owns the church building and cemetery lands and manages the site under the community park program. The cemetery is classified as a closed cemetery therefore no new additions to the grave sites are allowed unless previously reserved.
In 2012 structural renovations occurred to the church that consisted of raising the church and putting in a foundation and crawl space as well as upgrading the electrical system and installing a 2000 gallon cistern for a water supply to the washroom. In 2013 the church washroom was upgraded to current building code standards and a wheelchair accessible ramp was constructed.
The Mill Bay Church currently houses a museum and is used by the Mill Bay-Malahat, Bamberton and Cobble Hill historical societies.