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There was a church at Nether Poppleton from at least the eleventh century. It was appropriated to St Mary's Abbey, York, at its foundation in 1088 and the Abbey held the advowson until the Dissolution of the Monasteries in the sixteenth century, at which time it passed to the Crown and then to the Archbishop of York. It is not known when a vicarage was ordained there but it was described as such by the seventeenth century. The living was augmented in 1829.

The present parish church dates to the twelfth century. It is dedicated to the seventh century Saxon saint Everilda, who is believed to have led a monastic community at either Everingham or Nether Poppleton. The church was restored in the nineteenth century and in 1939 a new altar was installed, carved by Robert 'the Mouseman' Thompson of Kilburn. In 2015 an extension was added to house new kitchen and storage facilities.

In 1866 Upper Poppleton chapelry separated from Copmanthorpe parish to join that of Nether Poppleton. Today Nether Poppleton is part of the united parish and benefice of Nether with Upper Poppleton.

Upper Poppleton was originally a chapelry within the medieval parish of York, St Mary Bishophill Junior and thus subject to the peculiar jurisdiction of the Dean and Chapter of York until the nineteenth century. In 1844 the chapelry became part of a new parish of Copmanthorpe with Upper Poppleton, and then in 1866 it separated from Copmanthorpe to join the existing parish and benefice of Nether Poppleton, which became Nether Poppleton with Upper Poppleton.

The present church, which is dedicated to All Saints, was built in 1890 by architect Charles Hodgson Fowler, replacing the medieval chapel of All Hallows. The church was altered in 1959-1972 by George Pace.