The church, with a dedication to St John, was opened for worship in 1809 and consecrated in 1815. Originally the pulpit was half way down the north wall and the altar opposite on the south side. The entrance doors were at either end of the building and there were galleries at the east and west end. The interior was re-ordered in 1885, by Captain Stewart of Fasnacloich, when the dedication was changed to comemorate the arrival of the faith at this point on the mainland, closest to the island of Lismore where was the community of St Moluag in Pictish times and which, in the twelfth century, saw the building of the first Cathedral of Argyll. The village of Portnacrois also derives its name from this historic mission.
At some date a large wing was added to the north of the church which may originally have been used as school-rooms, but was also used as a house for the priest at one stage.
St Mary’s, Glencreran, was built in 1878 by Captain Stewart of Fasnacloich to replace the Fasnacloich school-house to which services were transferred from the old chapel at Glasdrum, demolished in the 1850’s. A rectory adjoined the church, to which a chancel was added in 1883, but the whole was closed in 1974 and sold.
In 1974 there was another re-ordering of the church to include features from St Mary’s, Glencreran, and the resulting plan reverted to one similar to the original design with the north wing after extension being partly opened into the church, and part used as a vestry.
In the church is a replica of the banner carried by the Stewart Regiment at Culloden; the original is lodged in Edinburgh Castle. Near this is a framed account of the Clan history during and after the battle, with a list of the casualties sustained by the Regiment. The wall tablets relate mainly to the Stewart families, some of these memorials having been bought to St Cross from St Mary’s along with some of the stained glass, when that church was closed. The small heraldic shields around the church include the arms of Stewart of Achnacone and the Diocese. The carpet, altar frontals and new tapestry hassocks are the work of current members of the congregation. In the church grounds, on the hillock to the south, stands a memorial to the Battle of Stalc in 1460, at which the MacDougall’s were defeated by the Stewarts of Appin.
The congregation was ministered to from Ballachulish until 1841, when a separate clergyman was appointed for Duror, Portnacrois and Glencreran. From 1878 to 1903 Portnacrois and Glencreran were independent, with the Rector living at Glencreran.