File:Interior, Holy Trinity church, Micklegate, York (16724236792).jpg

The church dates from the late 11th and early 12th century, and was rebuilt after a fire in 1137, originally with a crossing c.1180 and nave with aisles of five bays. At the time, the church was part of a large ministry of the Benedictine order. The complex covered some 7 acres. However, most monastic buildings did not survive the dissolution of the monasteries in the 16th century, but the priory church was allowed to continue as a parish church.

In the mid-16th century the church was in disrepair and stones were taken to repair the Ouse bridge and city walls. The north aisle does not exist today, but the piers are still visible. The south aisle is still extant with 13th century piers. The Eastern arm of the church which was aisled with five bays has completely gone, as have the transepts. The western Bay of the north aisle contains the St Nicholas Chapel from 1453, the tower was built above this on 13th century footings and is topped with a battlemented parapet.

Major restoration began in 1850 when a new south aisle was built and new chancel and vestry built in 1886.

The church has east and west windows by Kempe, and several monuments and floor slabs from the 18th and 19th-century.