In 1207-8, Bishop Brice Douglas chose the church at Spynie as his cathedral. Although his successor moved the bishop’s seat in 1224, to a new cathedral in Elgin, the bishops continued to live at Spynie.

Nothing remains of the original 13th century timber buildings, and very little remains of the stone buildings which replaced them in the 14th century. Most of the palace dates from the 15th century and later.

The large tower house at the southwest corner of the palace was begun by Bishop David Stewart (1462-77) and completed by his successor, William Tulloch (1477-82). It is one of the largest tower houses in Scotland and originally contained five floors above a vaulted basement. The remains of an earlier circular tower can be seen in the basement, but all the floors above ground level are now missing, although it is still possible to climb to the roof.

By 1500 the layout of the palace was very much as it appears today. Rectangular towers had been constructed at two corners of the courtyard, there was a new gateway on the east side, and a large hall had been built on the north side.

The last Catholic Bishop to reside at Spynie was Bishop Patrick Hepburn (1538-73), who was responsible for a remodelling of David’s Tower. Following the Reformation, Protestant bishops continued to live at Spynie until 1689 when episcopacy was abolished in the Church of Scotland. Bishop William Hay was deprived of his office and the palace fell into decay.