The Reformation meant that most of the properties previously owned by the Catholic church were seized by the crown and redistributed to private ownership. Monkton House passed to Mark Ker, previously the lay Abbot of Newbattle Abbey, who renounced Catholicism in favour of Protestantism. As a reward, he was granted the vast tracts of land belonging to the Abbey.

His son, also named Mark Ker, became the 1st Earl of Lothian. His daughter, Margaret, married James, 7th Lord Hay of Yester. Our theory is that Monkton House may have been part of her dowry, and that is how it passed into the ownership of the Hays of Yester.