Despite its new found pilgrimage potential however, the church at York lost its cathedral status to Lindisfarne in Northumberland the following year. Thirty years of obscurity followed, until St. Wilfrid persuaded the Northumbrians to switch from Irish-based  to Roman Catholicism. Being highly influenced by Rome itself, which he had visited, Wilfred preferred the urban setting of York to rural Lindisfarne. Upon becoming Bishop of York in AD 664, he found the minster in a state of disrepair: "The leaking roofs admitted rain and the open windows, birds who built their nests within and were constantly flying in and out. The rain and the birds, together, defiled and discoloured the neglected walls."  But he did not repair the structure as his new cathedral with whitewashed walls of lime until his return from a European tour in AD 669. He had the roof releaded and glazed the windows for the first time. It may have been at this time that the little used Royal palace surrounding the cathedral was handed over to Episcopal control, while the Kings of Northumbria built a new residence around the the south-east gate of the old Roman fort. This area is now called 'King's Square' although the name may only date from the Viking period.

For almost the next hundred years, the cathedral and the diocese flourished, culminating in Bishop Egbert being raised to the Archiepiscopate in AD 735. Bishop Wilfred II had refurbished the cathedral in the AD 720s; but, on 23rd April AD 741, the church, or at least part of the Archiepiscopal complex, was apparently destroyed by fire. It must have been pretty devastating, for the place was apparently not rebuilt until Bishop Albert came to the Archiepiscopal throne in AD 767. Though it is just possible the description is of Holy Trinity Priory in Micklegate, the cathedral's famous schoolmaster, Alcuin, appears to describe this building in his poetry:

"A new structure of a wondrous basilica was in the days of this bishop began, completed, and consecrated. This house of appropriate altitude is supported by solid columns set under curved arches. Within it sparkles with admirable ceilings and windows, and in its beauty shines, environed with many aisles (or apsidal chapels). It has a great number of apartments with distinct roofs, which contain thirty altars with various ornaments. Two disciples, Enbald and Alcuin, at the command of the prelate erected this temple, and he himself consecrated it to the Saviour ten days before his death."

Another associated building of note was a small bellcote with two large bells. The trappings within were described thus:

"The bishop had constructed a large altar and covered it all about with gold and silver and jewels. He dedicated it to the name of holy Paul; He suspended above this altar a lofty candelabrum, which sustained three large vessels for oil with nine rows of lights. He raised the banner of the cross aloft the altar, and covered the whole with precious metals.... And he made another altar, and clothed it with pure silver and with precious stones, and dedicated it to the martyrs and to the cross."

The high number of chapels can probably be explained by the use of multi-storied galleries. Bishop Albert crowned King Erdwulf of Northumbria in one of these dedicated to St. Paul in AD 796. The cathedral's school and library were the envy of all Europe at this time. However, when the Vikings took York in AD 866, the buildings were sacked and the library dispersed, if not destroyed. The cathedral was in decline. Later, however, constitutional changes forced upon the complex, and instigated by Bishop Wulfstan II, led Bishop Aeldred to undertaking considerable new building work.

Important Burials in the Saxon Cathedral include: King Edwin's Head (AD 632), King Aelfwin (AD 678), Archbishop Egbert (AD 766), King Edbert (AD 768), Archbishop Enbald I (AD 796), King Osbald (AD 799), King Guthfrith (AD 895), King Sweyn (temporarily in AD 1014) and Archbishop Aeldred (1069). It survived until 1069 when it was destroyed by the ravaging Vikings.