A medieval coped grave stone at Dunkeld is kept in the ground-floor space of the W tower of the former cathedral church. On one side of the stone a tesselated pattern has been cut in, while carved on the other side is a stepped, Calvary base and a section of shaft for a cross (the top of the cross no longer exists). The stone seems to have been moved from the graveyard into the tower (Simpson, p. 20), but nothing appears to be known about it prior to its removal. Within the actual building fabric of the church, nothing earlier than the 13th century survives. After the Reformation, the church was allowed to fall into ruin, except for the chancel which was used as the parish church. In 1689 most of the town was destroyed and burned. At the same time, Bishops of the cathedral were abolished. Repairs were made to the eastern end of the church in 1691 and again in 1792. In 1814-15, the former cathedral church received extensive restoration work. More restoration work was carried out in 1908.

Dunkeld is the site of an early religious community, where Constantine (king of the Picts 789-820), son of Fergus, seems to have built a church. From the early part of the 9th century, Dunkeld appears to have been the superior Pictish church, but at the end of that century the primacy was transferred to Abernethy. It is written that the relics of St Columba were taken from Iona to Ireland in 849 for protection and thereafter transferred to Dunkeld by Kenneth MacAlpin (reigned 843 to 858). The church at Dunkeld was part of an abbey at this time. 'Tuathal mac Artguso' is listed as abbot and bishop, dying in 865. Abbots of Dunkeld are recorded until the end of the 11th century, when Ethelred, abbot of Dunkeld, died. Etherlred was the son of King Malcom III and Queen Margaret. He was also Earl of Fife. The diocese was revived during the reign of King Alexander I (1107-24), Cormac being the first bishop mentioned. Cormac, a bishop, witnessed the foundation charter of the Scone Abbey in 1114/1115 , but Dunkeld is only specifically named as his bishopric in 1127-29. Very little is known about Cormac or his successor Gregory (d. 1169), both of whom are known as witnesses to various charters. Where they were buried is unrecorded. After Bishop Gregory, Richard, who was chaplain of the king, was bishop 1170-8. He, along with King William I of Scotland, swore allegiance to the English king (Henry II) in 1175. According to Mylne (writing in 1555), Richard was buried at the priory of Inchcolm, part of the medieval diocese of Dunkeld. Thereafter a dispute arose about the election of the next bishop, which appears to have left the see void for several years. John Scotus was elected in 1178 and consecrated in 1180, but he failed to take possession of the see until 1183. During his episcopate, the see of Dunkeld was divided into two, the west part becoming the bishopric of Argyll (later called Lismore). Bishop John died in 1203 and was buried at Newbattle Abbey. Bishops Richard II (d. 1210) and John II (d. 1214) are known to have been buried at Inchcolm Abbey. It is not stated where Bishop Hugh (d. 1229) was buried, but Bishop Gilbert (d. 1236) was also buried at Inchcolm. Under Gilbert and his successors, a chapter of secular canons was established at Dunkeld. Mylne states that Bishop Geoffrey (d. 1249) brought in the Rule of Sarum (Salisbury). He may have been responsible for construction of the earliest parts of the present choir and was buried in his cathedral church. Geoffrey was followed by Bishop Richard (d. 1272) whose body was buried at Dunkeld, but whose heart was interred in the N choir wall at Inchcolm, which he had caused to be built. Work on the cathedral church of Dunkeld continued into the Reformation. The earliest surviving effigy of a bishop is thought to represent Bishop Sinclair (d. 1337).

References to a church dedicated to The Holy Trinity at Dunkeld began to appear in the mid-12th century. It was given to Dunfermline Abbey in the early 1150s, but after 1234 it disappeared from the records.

Coped grave covers with tegular carving can be found at least as early as the Roman period. In England and Scotland it's first use in medieval times is usually associated with hogback and Pictish monuments. Dunkeld's grave cover has pointed 'tiles' which seem to be a later development of this type of funeral stone. Examples of other grave covers of this specific type within the British Isles have not been forthcoming. In Scotland, a small fragment of a coped grave cover in storage at Abercorn has carved tegulation with slightly-pointed tiles, but the form of these is rather different to those on the Dunkeld stone. In fact, the Dunkeld tile type can be more closely compared with tomb covers from the Roman and Early Christian Period on the continent (compare, for example, the tomb of St Andeol at Bourg-St-Andeol, France). Dating the Dunkeld stone is difficult. It is clearly not Roman, as shown by the cross, and is likely to be later than the coped grave covers that have had dates suggested into the early part of the twelfth century. Coped grave covers continued to be used throughout much of the medieval period in places. On coped grave covers, the practice of using one coped side to display a full cross (or other symbol) first appears in the second half of the twelfth century, an example of which is that preserved at St Aidan's Church, Bamburgh. Ryder (2003, p. 95) suggests a date of the late-12th or early-13th century for the Bamburgh grave cover. Moderately-sized roll mouldings carved along the lower coped edges and around the outer edges of the end faces is a development generally associated with the 12th century, appearing more commonly in the later 12th century and thereafter. Two such coped grave covers with this type of roll-moulded framing are preserved in storage at Durham Cathedral, one distinctly 12th century and the other no earlier than the late 11th century (and quite likely to date from the 12th century). A coped grave cover with raised decoration in storage in Dundee, thought to date from about 1200 or slightly later, has very similar roll-mouldings to those found on the Dunkeld coped stone. Simpson (p. 20) suggested an 'early date' for the Dunkeld example, while Fawcett (for The Society of Friends of Dunkeld Cathedral) stated that it 'may be as early as the twelfth century'. A date in the late-12th or early-13th century for the Dunkeld grave cover seems plausible. The direct source of inspiration for it, however, remains uncertain.

The references to the church of The Holy Trinity may refer to a parish church in Dunkeld. This church was given to Dunfermline Abbey between 1150 and 1153 by Andrew, bishop of Caithness, who may have resided in Dunkeld for part of his episcopacy and certainly spent most of his time in the southern half of Scotland, as opposed to his own diocese. He may, in fact, have been only titular bishop of Caithness, as Caithness appears to have been served by the bishopric of Kirkwall at this time. It has been suggested that Holy Trinity church was later subsumed into the cathedral church (Cowan, p. 53). The centre of the diocese of Caithness moved from Halkirk to Dornoch (both in Caithness), where a cathedral church was built about the same time that the church of The Holy Trinity disappears from the records.