In 1890, 75 members of St. Paul's Church (founded 1867) in Old Decatur, split away from the church over the location of a new building. Newcomers to the parish and city wanted to build it in New Decatur/Albany, near their homes. Longtime St. Paul's members preferred the Old Decatur location. So a second parish, St. John's was established and admitted to the Diocese of Alabama in 1891.The women of the parish formed the Guild of St. John's Church in 1891, and worked tirelessly through the decades to meet the needs of the new congregation. The all-male vestry set the direction of the church, but regularly requested monetary and volunteer assistance from the Guild, which raised money by making and selling homemade ice cream, cakes, and aprons. The Guild is credited with keeping St. John's afloat as the new church struggled financially. The first woman was elected to the vestry in 1973.
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On February 19, 1893, the growing congregation dedicated its first church, a Gothic-style wooden edifice erected for less than $2,000. This building, which originally faced Jackson Street, was turned ninety degrees westward to face Second Avenue in 1940. Now encased in stone, the 1893 building forms the nucleus of the present church. A tall central entrance tower and needle spire were added in 1948, lending to St. John's something of the character of a small 16th-century English village church.A parish house, built in 1955, was enlarged and renovated in 2007, along with the church itself. In 1999, St. John's purchased the old Baugh-Wiley-Smith Hospital to the rear of the church and established the Episcopal Center. The Center houses the first free community health clinic in Decatur, along with other non-profit organizations.In 1983, St. John's was listed in the National Register of Historic Places as part of the New Decatur/Albany Residential Historic District.