The now demolished St. Mary Bishophill (Senior) Church dated to before the Norman conquest times, and had a nave which was of a late Saxon date, and the church was also recorded in the Domesday Book. An aisle was added in the twelfth century and a doorway from the same period which survived until the church was demolished in the 1960s. It has also been discovered that there were also some Roman walls situated underneath the church.

On the 17th January 1585 the parish of St. Clement without Skeldergate was united to this parish. In 1659 the bell-house was demolished and replaced by a new steeple.
Although abolished in 1868, church rates existed before then, which was a charge levied on the ratepayers of a parish to fund the local church. In1857 the church rate for St. Mary's was rejected by ratepayers and the church needed to secure the funding by voluntary subscription.

In June 1859 the church was closed to allow for a major restoration, the interior was gutted, new seats were installed, a new organ introduced and the windows were reglazed. The changes cost a total of 500 pounds and the church re-opened in February 1860.

Despite the Victorian renovations,the future of the church seemed bleak by the early twentieth century as the size of the congregation started to fall. In 1931 the Church Commissioners recommended demolishing the church and turning the graveyard into a public park. The Reverend A Raine said about the demolition proposals, "this would be a tragedy for it is one of York's oldest churches, Roman stones were used in its walls and a grave slab of a pre-Norman ecclesiastic was still to be seen. The church contains examples of Norman Early English and other forms of architecture".

In the late 1950s a faculty was given to demolish the church, but there was substantial local concern over the destruction of the church. A local vicar, RCJ Wilkins, suggested that one of the redundant churches in the city could be rebuilt to become the parish church of Holy Redeemer on Boroughbridge Road in Acomb. A suggestion was made by the architect George Pace that the church's unique windows from the twelfth to fifteenth centuries, the transitional doorway, the piscena and altar slab could be incorporated in the move.

The church was sadly demolished in 1963 and some of the fittings were moved to St. Clement's Church on Scarcroft Road and the arcade was incorporated into the Church of the Holy Redeemer on Boroughbridge Road. In 2010 a group of volunteers decided to form a gardening group to tidy up the church's old graveyard which, although under the control of York City Council, had become overgrown. The Archdeacon of York, Mr Kilbane, said the church approved of the work, but noted that "we need to respect the fact that it is a graveyard and an important archaeological site, so no digging too deep or planting vegetables".