The nave of the church was consecrated by Bishop Harper on 25th March 1879. At the time it was beyond the means of the congregation to fund more of the build but by 1890 the Chancel, porch and vestry were added and the church was complete.
In the 10 March 1909 edition The Otago Witness, featured an article about some bees, “which for many years have made their home at the entrance to St. John's Church, Winchester, and which have resisted all attempts to dislodge them, are a source of much annoyance to the churchgoers. On Sunday (says the Temuka Leader) last two persons were stung by them.”
By the 1960’s attendance began to decline and the decision was made to unify the Presbyterian and Anglican parishes with activity being centred on the Presbyterian Church Hall. St John’s church became redundant.
From 1907 until the mid-fifties the pupils from Waihi School used to march down the main road each Sunday morning to attend the service smartly dressed in their uniforms and sporting cream ‘boater’ hats. There were close links with St John's Anglican Church from the earliest days of the school with the Headmaster, Joseph Orford, conducting many of the services as the vicar from Temuka was only scheduled to visit once a month.
In 1971 the Anglican Parish offered their old church buildings to Waihi Preparatory School, covering the cost of moving it to its new location, carrying out repair work and finally repainting the church as part of the gift. By 1972 the old church had been moved into its new surroundings, the pupils used the church daily before school and the cream ‘boater’ hats became redundant in the process.
This building enjoys a Heritage 2 listing with Heritage New Zealand.