Although the patron Saint of the Seton Family has always been St. Benedict (called St. Bennett's in war-cry) the Seton Church was dedicated in the names of St. Mary and the Holy Cross, and was begun in the thirteenth century. In 1390, a south aisle was built by Catherine Sinclair, widow of William, the First Lord Seton and slightly added to by John, 2nd Lord Seton.

The Church was created a Collegiate Church on 20 June 1493 by George 3rd Lord Seton, and additions were made by George, 4th Lord Seton, as well as George 5th Lord Seton and his Lady Janet Seton (Hepburn) who generously endowed the Church.

In 1544 it was damaged during the English invasion of the Earl of Hertford, and in 1580, the Church was united with Tranent under George 7th Lord Seton and was well patronised until 1715, when it was entered by the Lothian Militia, and incited that Lord Winton was a Jacobite, the Militia defaced the interior and demolished the tombs, the remains of those actions being apparent today.

Although preserved by the Earl of Wemyss during their ownership following the Seton forfeiture, the interior was repaved by them and many of the important Seton monuments were buried under the new floor.  What is presented today, are remains of the Seton memorials, and fragments of grand oriel window of the entrance block that was demolished in the raids of 1715.