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The First Presbyterian Church service in the Papatoetoe area was by the Rev. John Macky on 27 August 1854 at Baird's storage shed near the Tāmaki River. Rev. Macky is buried in the cemetery at St Johns Presbyterian Church, 120 Great South Road along with many well-known Papatoetoe and East Tāmaki people, including Thomas Baird, who donated the land for the church. The present St Johns Presbyterian Church is the third church on the site. The original was built in 1855 - first known as the Otahuhu Presbyterian Church, then as the Otara Presbyterian Church, and from about 1907 as the Papatoetoe Presbyterian Church.

Prime Minister William F. Massey laid the foundation stone of the present church on 30 December 1922. In January 2011 the church and community centre were rededicated after significant architectural alterations including a new roof, a linked foyer and 6m high stained glass doors depicting the burning bush with frangipani flowers and inscribed with the 23rd psalm. Corten steel shutters, each weighing 0.5 tonne, protect the stained glass. Silhouettes of kanuka trees, present in Aotearoa New Zealand before European settlement, are patterned in perforations on each shutter.