It remained unscathed during the Wars of Scottish Independence but suffered extensive fire damage in 1390 when attacked by Robert III's brother Alexander Stewart, Earl of Buchan, also known as the Wolf of Badenoch.

[13] Simon's successor was Richard of Lincoln, once again a royal clerk, and one who struggled to build up the revenues of the bishopric during and after the insurgence of Domnall mac Uilleim (Donald MacWilliam).

[14] On 7 April 1206, Pope Innocent III issued an apostolic bull allowing bishop Brice de Douglas to fix his cathedral church at Spynie.

[14] On 5 July, Alexander II (Alaxandair mac Uilliam) agreed to the transference in a writ referring to his previous land grant for this purpose.

[10] Soon after his election to the see in 1362–63, Bishop Alexander Bur requested funds from Pope Urban V to repair the cathedral, citing neglect and hostile attacks.

[23][24] In response, and possibly through frustration of the reappointment of his brother Robert Stewart, Earl of Fife as guardian of Scotland, Buchan descended from his island castle on Lochindorb and burned the town of Forres in May and Elgin, including the cathedral and its manses, in June.

[27] Bur sought reparation from Robert III for his brother's actions in a letter stating:[10] my church was the particular ornament of the fatherland, the glory of the kingdom, the joy of strangers and incoming guests, the object of praise and exaltation in other kingdoms because of its decoration, by which it is believed that God was properly worshipped; not to mention its high bell towers, its venerable furnishings and uncountable jewels.Robert III granted Bur an annuity of £20 for his lifetime, and the Pope provided income from the Scottish Church over the following decade.

[32] Bishop John Innes (1407–14) made significant contributions to the cathedral's rebuilding efforts, as evidenced by the inscription on his tomb praising his work.

Upon his death, the chapter met secretly—"in quadam camera secreta in campanili ecclesie Moraviensis" ("in the same secret chamber in the bell tower of Moray church")—and agreed that if one of its members was elected bishop, they would provide one-third of the bishopric income annually until the reconstruction was completed.

[14] His successor, Bishop Andrew de Moravia expanded the chapter significantly by appointing two additional senior positions (succentor and subdean) and 16 more canons with prebends.

[46] Mensal prebends: Large cathedrals such as Elgin had many chapel altars requiring canons, assisted by many chaplains and vicars, to conduct daily services.

[31] In 1350, the stipends of the vicars at Elgin were not sufficient for their livelihoods, so Bishop John of Pilmuir provided them with the income from two churches and the patronage of another from Thomas Randolph, second Earl of Moray.

In the Diocese of Aberdeen, and likely in other bishoprics as well, when important decisions needed to be made by the chapter, an absentee canon had to appoint a procurator to act on their behalf.

[58] Much of the workload fell on vicars and a smaller number of permanent canons who were responsible for celebrating high mass, delivering sermons, and organising feast day processions.

[63] It is constructed from a 19th century Ordnance Survey (OS) town map of Elgin as its base layer and preserves the road layout which has changed little since medieval times.

[81] Andrew also instructed thirteen prebendaries, which included the archdeacon and the succentor, to immediately "erect, construct, build, and duly repair their manses, and the enclosures of their gardens within the college of Moray".

[89] The hospital of Maison Dieu, dedicated to St Mary, was situated near the cathedral precinct and was established by Bishop Andrew de Moravia before 1237 for the aid of the poor.

[92][93] In August 1560, parliament gathered in Edinburgh to enact legislation declaring the Scottish church to be Protestant, removing papal authority, and making the Catholic mass illegal.

[98] In 1640 the General Assembly ordered Gilbert Ross, the minister of St Giles Kirk, to remove the rood screen partitioning the choir and presbytery from the nave.

[103] By the closing years of the 18th century, travellers to Elgin began to visit the ruin, and pamphlets giving the history of the cathedral were prepared for those early tourists.

Acknowledging the necessity to stabilise the structure, the Elgin Town Council initiated the reconstruction of the perimeter wall in 1809 and cleared debris from the surrounding area in about 1815.

[105] The Lord Provost of Elgin petitioned the King's Remembrancer for assistance to build a new roof for the chapter house and in 1824, £121 was provided to the architect Robert Reid for its construction.

A fortnight later, the Inverness Courier published a commemorative piece on Shanks, calling him the "beadle or cicerone of Elgin Cathedral", and writing:[107] His unwearied enthusiasm in clearing away the rubbish which encumbered the area of the Cathedral and obscured its architectural beauties, may be gathered from the fact that he removed, with his pick-axe and shovel, 2866 barrowfuls of earth, besides disclosing a flight of steps that led to the grand gateway of the edifice.

Tombs and figures, which had long lain hid in obscurity, were unearthed and every monumental fragment of saints and holy men was carefully preserved, and placed in some appropriate situation ...

The bishops, representing religious and secular authority, played an important role in solidifying royal governance and stability in a historically volatile region.

The importance of this relationship was recognised on 8 November 1451 when James II provided Bishop John Winchester with the Barony of Spynie enabling the consolidation of the disparate church lands and other properties into a single entity.

This provided the bishop with wide-ranging powers including the convening of courts of law capable of adjudicating crimes that had previously fallen solely under the jurisdiction of the king's legal officer, the Sheriff.

While the 1390 fire destroyed many charters that likely contained significant details regarding the attainment of land grants from royalty and the aristocracy, the surviving documents offer valuable insights into this process.

The lands extended southwards into the highland territories on the river's upper reaches of Strathspey and in its catchment area spreading as far south as Logynkenny near the diocesan border with the lordship of Lochaber.

[114] The north wall of the choir is the earliest extant structure, dating to the years immediately after the church's 1224 foundation; the clerestory windows on top of it are from the later post-1270 reconstruction.