This congregation was organized as Ascension Church on April 4, 1856. Led by then-deacon David Knickerbaker, the church became so closely identified with the Reverend Knickerbaker that it was often called Knickerbaker's church. The congregation met for several months in a hall on Helen Street (later renamed 2nd Avenue South), and erected a church at 5th Street and 7th Avenue South and dedicated on August 5, 1856, the first religious building erected in Minneapolis. In 1857, the congregation added a bell tower to the building and changed its name to Gethsemane. In 1883, the congregation began erecting a new church at 4th Avenue South and 9th Street, designed by architect Edward S. Stebbins. They dedicated the new church on February 16, 1895. The nearby parish house was decidated on February 16, 1895, and Knickerbacker Hall on May 1, 1927.
The congregation founded several other organizations. The Brotherhood of Gethsemane, a benevolent organization of local businessmen, founded Cottage Hospital, later renamed Saint Barnabas Hospital, the first hospital in Minneapolis, in 1871. In 1882, they founded an orphan's home. Several missions and daughter parishes were also founded by Gethsemane: St. Mark's Episcopal Church (1868), the Chapel of the Brotherhood (1868), St. Andrew's (founded as a mission in 1870, and established as a parish in 1875), Shingle Creek Mission in Saint Paul (1869), Trinity Church in the Oak Grove neighborhood (1869), All Saints (1871), Parker's Lake (1871), All Saints at Howards Lake (1871), Mission of the Holy Spirit in Delano (1906), Grace Chapel (1877), Saint Jude's, connected to Sister Annett's Baby Home in Elliott Addition (1877), Saint James (??), St. Mark's Corinna on Clear Water Lake (1877), Holy Innocents Chapel founded in connection with Sheltering Arms (1883), Mount Calvary --later renamed Saint Luke's (1885), Minnehaha Mission (1887) Epiphany MIssion (1893), Trinity Chapel at Excelsior (1891), Shepherd's Fold (1894), Prospect Park Mission (1896), Saint Thomas Mission (African American), (1899), (this group first met in a store on 6th Avenue South near 7th Street but later moved to the former Swedenborgan Church at 5th Avenue South and 9th Street, which they rented), and Saint John's Mission in Linden Hills (1901).