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 the first bishops were based on a misinterpretation and reliance on the early charters found in the cartulary of Aberdeen Cathedral. These charters are now known to be false. The first recorded bishop of the diocese was Nectan, mentioned in the Book of Deer around 1132. The earliest direct written evidence of a bishop in Aberdeen appears in a papal bull addressed to Bishop Edward in 1157. This bull acknowledged the existence of his cathedral, discussed the formation of a chapter, and marked the beginning of the diocesan expansion.

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’ patronage shifted to cathedrals and monasteries, enriching these institutions at the expense of the parishes. The cathedral, with its expanding number of canonries, used the appropriated income to sustain itself. The beneficiary canons had a duty to ensure an income for the parish vicars although the stipends were generally meagre.

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

The likely mythic origins of the diocese are found in the cathedral's chartulary which identified the early bishops—Bean, Denortius, Cormac and Nectan—with Mortlach, in present-day Moray. This tradition rests on a series of early charters that are acknowledged to be false. These charters allowed Hector Boece to construct a history that had successive Mortlach bishops, culminating with its fourth prelate, Nectan, who would then move his see to Aberdeen. Beyond his appearance in one of these spurious charters, Nectan is only once documented as bishop of Aberdeen—in a small note (c. 1132) found in the Book of Deer. Nevertheless, Mortlach did possess early ecclesiastical significance. A Papal Bull of 1157 by Pope Adrian IV confirmed the existence of a monasterium at Mortlach along with five attendant churches as part of the diocese of Aberdeen. By the 11th century, this type of organisation was characteristic of Culdee (Céli Dé) settlements—the Culdees resembled communities of secular priests ministering to local populations but directed from the central mother church (the monasterium).

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. 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. 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 leading to a diminished importance of mother churches. The strongest stimulus for change took place under the influence of King David I. He introduced an ordinance that guaranteed the rights of the parochial churches and their priests who were to be sustained by the collection of teinds. Consequentially, and particularly in areas of extensive feudal expansion by Anglo-Norman lords (such as in the diocese of Aberdeen), geographically based and viable parochial entities emerged within the diocese. These local lords—with some regard for the hereafter—granted their right of patronage over parish churches to the cathedral or a monastery of their choosing. This, combined with the establishment of new monasteries, considerably impacted upon the Culdee mother churches and pendicle churches. Some were reduced to ordinary parish churches, such as Mortlach and Cabrach, while others, more rarely, transformed into organisations that more closely resembled their former existence. For instance, Monymusk became a house of Augustinian canons regular.

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. 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.

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.

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. Additionally, 42 other parish churches were appropriated to monasteries and other ecclesiastical foundations, leaving only 4 parishes—Cushnie, Forvie, Tough, and Tyrie—as independent entities. 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 Cistercian monastery at Deer. Furthermore, the Carmelite, Dominican, Franciscan, and Trinitarian Friars all had houses in Aberdeen itself.