Just south of the present church is a small building orientated north-south, the north entrance of which is built using several reused medieval stones. This doorway, which is segmental headed, has two orders and a label. Decorative features include two broadleaf capitals, dogtooth and filleted-roll voussoirs. The parish church at Clunie, in the district of Stormont, was rebuilt in 1840, replacing a church reportedly built “about the time of the Reformation” which had, itself, been repaired in 1788. This earlier church was said to have “neither comeliness nor proportion” (McRitchie, 1793 Statistical Account). It is unknown for certain the original location of the medieval, re-used stones, but it is assumed that they were part of a previous church on the site, although the possibility of their coming from the former castle cannot be discounted.

The earliest known reference to Clunie seems to occur in the mid-9th century in reference to Kenneth McAlpin, king of the Picts, who was at that time at war with the Britons. It has also been suggested that there was a royal hunting lodge at Cluny and that later, probably in the 12th century, a natural hilllock was used as a motte, the castle and church both being sited on the west bank of Loch Clunie. A grant of 1141 appears to have been given while King David I was at Clunie. King Edward I of England occupied Cluny Castle in 1296, and in 1377 John de Roos was appointed keeper of the castle by king Robert II of Scotland. The castle was replaced in the late 15th/early 16th cenutry by another castle on a new site on an island in Loch Clunie, its chapel dedicated to St Catherine. It seems likely that this work was undertaken for George Brown, bishop of Dunkeld 1483-1515, and was used at times by the Earls of Atholl. Stones from the earlier castle seem to have been re-used in its construction. The earliest known specific reference to the parish church at Cluny, however, only comes in the 13th century. Alexander Myln wrote that Geoffrey, bishop of Dunkeld 1236-49, annexed the church of Clunie to serve as a prebend of the dean of Dunkeld. This situation was repeated in Bagimond's Roll later that century: "Prebenda Decani cum ecclesiis de Inchecad et Clony". One hears nothing further about the church until the 15th century. In 1490, an altar dedicated to the Blessed Virgin Mary in the parish church at Clunie was mentioned.

A number of suggestions for the original purpose of the small building with re-used medieval stones have been put forward, including a sacristy, a chapel, a mausoleum and a watch house.

A parallel for the extended foliate decoration of the imposts of both capitals can be found in rare instances elsewhere, as at Coldingham Priory in the Scottish Borders. There they can be found on the interior of the surviving east interior wall. Simple waterleaf forms also appear on this wall, on the exterior. Moreover, on the same wall, found amongst the various other forms are keeled rolls with deep cavities along the side. There are slight differences of opinion as to the likely date of this specific work at Coldingham, with some suggesting the early part of the 13th century, and Fawcett and others suggesting the later-12th century. Stylisticallly, a date of around 1200 would fit the various carved forms re-used on the later-created doorway at Clunie. Some writers have proposed that the Clunie capitals and arches may have been used in different places within the church and that the capitals might be earlier than the arches, the former possibly dating from the late-12th century and the arches from the earlier part of the 13th century. Dates put foward by others for the various fragments range from the late-12th century to the early-13th century.