The Diocese of Aberdeen was originally believed to be the direct continuation of an 11th-century bishopric at Mortlach in present-day Moray. However, this early date and also the first bishops were based on a misinterpretation and reliance on early charters found in the cartulary of Aberdeen Cathedral that are now known to be false. The first recorded bishop of the diocese was Nectan, who was mentioned in the Book of Deer around 1132. The first direct written evidence of a bishop in Aberdeen is found in a papal bull addressed to Bishop Edward in 1157. This bull acknowledges the existence of his cathedral, discusses the formation of a chapter, and marks the start of the expansion of the diocesan structure.

The parochial system in Scotland had been developing since the early Middle Ages and saw significant progress under David I. He clarified the rights of the local church in terms of territory and jurisdiction. His reforms ensured that parishioners could support their priests by providing tiends, while local lords retained their rights to build churches and appoint priests. Over time, the lords’ rights to patronise churches shifted to the cathedral and the monasteries, enriching these institutions at the expense of the parishes. The cathedral, with its expanding number of canonries, used the appropriated income to sustain them. The beneficiary canons had a duty to ensure an income for the parish vicars but the stipends were generally meagre.

Reconstruction of the cathedral commenced in the late 14th century and extended into the 16th century.

The probably mythic origins of the diocese are contained in the cathedral's chartulary and identify the early bishops—Bean, Denortius, Cormac and Nectan—with Mortlach, in present-day Moray.^[1] This tradition was seemingly based on a series of early charters that are acknowledged to be false.^[2][3][4] These charters allowed Hector Boece to construct a history that had successive Mortlach bishops, ending with its fourth prelate, Nectan, who then moved his see to Aberdeen. Outside of his appearance in one of the spurious charters, Nectan is only once documented as bishop of Aberdeen in a small note (c. 1132) made in the Book of Deer.^[5]Despite this, Mortlach did possess early ecclesiastical importance. A Papal Bull of 1157 by Pope Adrian IV confirmed the existence of a monasterium at Mortlach with five attendant churches as belonging to the diocese of Aberdeen.^[6]By the 11th century, this type of organisation was characteristic of Culdee (Céli Dé) settlements—the Culdees resembled communities of secular priests who ministered to the populations but were directed from the central mother church (the monasterium).^[7]

Pope Adrian IV's bull of 1157 also confirmed to Bishop Edward the churches of Aberdeen, St Machar and St Nicholas, together with the town of Old Aberdeen and other lands.^[8][9] The bull authorised bishop Edward to establish a chapter in his cathedral, giving him the choice of introducing regular or secular canons as his clergy but nothing immediately came of this.^[10] The lack of a means of funding a fully functioning unit of clerics may have accounted for this. Reforms in the 12th century were partially driven by local landowners who provided churches and priests which in turn led to a lessening in the importance of mother churches.^[11] The strongest stimulus for change took place under the influence of King David I when he introduced an ordinance that guaranteed the rights of the parochial churches and their priests who were to be sustained by the levy of teinds. Consequentially, and particularly in areas of extensive feudal expansion of Anglo-Norman lords such as in the diocese of Aberdeen, had the effect of creating geographically based and viable parochial entities within the diocese. These local lords, with some regard for the hereafter, granted their right of patronage of the parish churches to the cathedral or to a monastery of their own choosing. This, taken together with newly founded monasteries, impacted upon the Culdee mother churches and pendicle churches to the extent that they were either reduced into becoming ordinary parish churches, such as Mortlach and Cabrach, or more rarely, were transformed into organisations that most closely resembled there former existence, i.e. as in the case of Monymusk, into a house of Augustinian canons regular.^[12]

The mechanism for the generation of income for the diocese was now available. The parish churches with their guaranteed income were soon to be the subject of appropriation by the large ecclesiastical corporations—the monasteries and cathedrals. At Aberdeen, the annexation process may have begun as early as Bishop Edward's tenure and increased in line with the development of the chapter.^[13] The enlargement was slow with incremental appointments of dignitaries continuing through to the mid-13th century when in 1249 Pope Innocent IV issued a bull to Bishop Peter Ramsay confirming the diocese constitution and a chapter consisting of five dignitaries and eight ordinary canonries all sustained on prebends.^[14]

Appropriation of parish incomes to prebendary canons in the cathedral weakened the parish churches. The cathedral canons, possessing the fruits of both the parsonages and the vicarages, were responsible for appointing vicars to the parishes. Invariably, the vicars were paid meagre pensions and lacked the security of tenure which resulted in inadequately educated clerics to deliver the cure of souls.^[15]

By 1488 the cathedral chapter had expanded to 29 canons supported by the income from 54 parish churches and of those, 42 were prebendal, one mensal and 11 held in common. 42 other parish churches were appropriated to monasteries and other ecclesiastical foundations and only 4 parishes—Cushnie, Forvie, Tough and Tyrie—remained independent. The diocese also included eleven hospitals/almshouses for the poor, aged or infirm parishioners. The religious Orders were also well represented—a Tironensian priory at Fyvie, a priory for Augustinian canons at Monymusk and a monastery at Deer for Cistercians. The Carmelite, Dominican, Franciscan and Trinitarian Friars all had houses in Aberdeen itself.^[16]

The reconstruction of the cathedral began when Bishop Alexander Kininmund (1355–80), probably nearing the end of his episcopacy, heightened the walls of the west towers and the nave. Bishop Henry Lichton (1422–40) completed what Kininmund had started and established the north transept but left the construction of the central tower incomplete. He was followed by Ingram Lindsay (1441–58) who roofed and paved the nave. Thomas Spens (1457–80) finely furnished the interior and Bishop William Elphinstone completed the central tower begun by Lichton. Elphinstone also commenced the rebuilding of a larger choir. The south transept was completed by Gavin Dunbar (1518–32) and provided the spires on the west towers. Dunbar was also responsible for the armorial adorned ceiling in the nave which displayed the coat-of-arms of the pontiff, the Scottish prelates and leading European rulers^{[17] [nb 1]}

The bishop held authority over the cathedral, parish churches, and hospitals. While the monasteries were largely independent of the episcopacy they still required the bishop if any of the brothers needed to be ordained to the priesthood. The monastic houses may occasionally receive patronage from the bishop and chapter.