The 1st Lord Seton introduced a college of priests in 1470 but it was his son who secured full collegiate status in 1492. The college comprised a provost, six priests, a clerk and two choir boys the ruins of whose accommodation is in the south east corner of the churchyard. The purpose of the college was to pray for Lord Seton and his family's salvation.
However the Protestant Reformation of 1560 effectively put an end to the church being used for masses sung for the souls of the Seton family. The building finally fell out of use around 1580 and was allowed to fall into decay. After the Jacobite Rebellion of 1715 the kirk was ransacked and the tombs broken open because of the Earl of Winton's support for the exiled Old Pretender, James Edward Stuart. Later that century the estate passed into the hands of the Earl of Weymss who restored what was left of the kirk as his family's mausoleum.