The origins of Bangor date back to the founding of a monastic establishment on the site of Bangor Cathedral by the Celtic saint Deiniol in the early 6th century AD.

In 973, Iago ab Idwal, ruler of the Kingdom of Gwynedd, was usurped by Hywel, and requested help from Edgar, King of England. Edgar, with an army, went to Bangor and encouraged both Iago and Hywel to share the leadership of the realm. Asserting overall control however, Edgar confirmed liberties and endowments of the Bishop of Bangor, granting land and gifts.

Bangor remained a small settlement, but development was spurred by slate mining at nearby Bethesda, beginning in the 1770s, becoming one of the largest slate quarries in the world.

The site of Bangor Cathedral was originally occupied by St Deiniol's Monastery. Deiniol is said to have been consecrated as a bishop by Saint David, making him the first Bishop of Bangor. This monastery was sacked in 634 and again in 1073. Nothing of the original building survives.

The Synod of Westminster in 1102 is recorded as taking measures to restore Bangor Cathedral, but the earliest part of the present building was built around 1130 with the assistance of the king of Gwynedd, Gruffudd ap Cynan, who donated money towards the project and was buried by the high altar on his death in 1137. This was a cruciform building in the Norman style. In 1211, the cathedral was destroyed by King John's army, on a raid into Gwynedd.

In the 13th century the original apse was removed and the choir was extended to its present length. The church was badly damaged when King Edward I invaded Gwynedd in 1282, and in 1284 the chapter wase given £60 in compensation for the damage. There was extensive rebuilding in this period, under the first Bishop Anian, with the transepts and crossing rebuilt. The nave was rebuilt in the late 14th century.

The cathedral was said to have been burnt to the ground in 1402 during the rebellion of Owain Glyndŵr, but there is no contemporary evidence for this. There certainly was extensive reconstruction from the end of the 15th century, completed in 1532.