From the Revolution until 1810, the congregation had no settled incumbent and was served by itinerant Gaelic speaking priests, such as The Rev’d Allan Cameron who, with Bishop Forbes, visited Ballachulish in 1770.
These visits ceased in 1784 when The Rev’d Donald MacColl, a native of Appin, was ordained for the district.
Bishop Forbes mentions in his Journal, that he preached to large gatherings from the doorway of a small storehouse.
This building was used during the Penal Laws, or people met secretly in caves or on the hillsides, and was gifted by John Stewart, Laird of Ballachulish House.
In the early years of the 19th Century, the storehouse was converted into a church and still stands in the Burial Ground.
During the Episcopate of Bishop Low, who succeeded Bishop MacFarlane in 1819 and often visited Ballachulish, the schools at Ballachulish & Lochaber were started. The Rev’d J R A Chinnery-Haldane, Rector 1879-85, built a new school & teacher’s house in Ballachulish.
The present Church was built in 1842 and consecrated in 1844, with a chancel being added in 1888. The first parsonage was built in 1838 followed by a new parsonage during the incumbancy of The Rev’d D MacKenzie 1861-79 (sold in 1976 when Ballachulish was linked to Glencoe).
St John’s is the “Mother Church” of the area and is in possession of the Altar Vessels inscribed “Parish of Appine, 1723”, which were purportedly used for Communion by the Jacobite troops on the evening before the Battle of Culloden in 1745.