Early in 1488 he was made Lord High Chancellor, but on the king's death in the following June he left office, and retired to Aberdeen.

[1]Having been made Keeper of the Privy Seal of Scotland in 1492, and having arranged a dispute between the Scots and the Dutch, Elphinstone's later years were mainly spent in the foundation of the University of Aberdeen.

The university, modelled on that of Paris and intended principally as a law school, soon became the most famous and popular of the Scots seats of learning, largely due to the prestige of Elphinstone and his friend, Hector Boece, the first rector.

Elphinstone also built the central tower of St Machar's Cathedral, and funded the building of the first stone bridge over the River Dee.

Continuing to participate in public affairs he opposed the policy of hostility towards England which led to the Battle of Flodden in September 1513.