The Augustinian monks of Holyrood Abbey held superiority over the church and likely founded it as a centre of education in the 13th century.

The church is also notable for its association with the murder of Henry Stuart, Lord Darnley, husband of Mary, Queen of Scots, which took place in the vicinity in 1567.

[1] It was dedicated to the Blessed Virgin Mary of Consolation and may have been established around the same time as the neighbouring church of the Blackfriars, which was founded in 1230.

[1][4] St Mary's appears to have been raised to the status of a collegiate church early in the 16th century.

[5][6] The church possessed a successful garden that stretched down to the Cowgate, incorporating the area now represented by Old College, Infirmary Street, High School Yards.

[2][4] The church also possessed a tenement dedicated to the altar of St Katherine, located in the Cowgate at the foot of what is now Blair Street.

[5] The Duke of Châtellerault purchased the remains of the hospital around 1551 and built a mansion noted for its gardens and painted windows.

[15][16] On 10 February, Henry Stuart, Lord Darnley, husband of Mary, Queen of Scots, was found dead in the vicinity of the church.

The explosion preceding Darnley's death destroyed the provost's house and several other buildings surrounding the church.

[19][21] The tower was taken down by Michael Hunter in 1616 and the last remnants of the church were removed around 1629, when the upper court of the college was terraced.

[22][23] The following clergy served as provost of the Collegiate Church of St Mary in the Fields, their names are given along with the dates which can be established for their provostries.

Richard Bothwell and John Spittal appear in litigation in 1543 over who was rightly provost, as did William Penicuik and Alexander Forrest in 1562–1563.

[24] Matthew Ker: 1511, 1512–1515 Richard Bothwell: 1523–1544 David Vocat: 1527 (ambiguous source) John Spittal: 1543–1552 William Penicuik: c1550–1563, 1566 Alexander Forrest: 1552–1561 Robert Balfour: 1566–1579 John Gibb: 1579– Only two contemporary illustrations of Kirk o' Field exist.

[29] In 2010, archaeological excavations of the quadrangle of Old College uncovered human remains believed to have been associated with the church.

The excavations found that the last remnants of the church had been removed with the lowering of the ground at the completion of Old College around 1832.