The church was built in memory of Allan Thom's father, Robert, who purchased Canna in 1881 and had invested in improvements to the island's infrastructure.

Although the church was built to serve the island's Protestant inhabitants, Canna was and is principally Catholic.

The church is orientated East-North-East to West-South-West, rather than the more usual East-West, though why this was done is unclear.

As most islanders are Catholic, St Columba's, whilst still consecrated for worship, is rarely used and is all but defunct.

In 2015, it was reported that the National Trust for Scotland were seeking funds to repair the church and use it as an exhibition-space for memorabilia from the 1881-1938 period.