The church became caught up in an 1140 dispute over the bishopric of Durham following the usurpation of the diocese by William Cumin, Chancellor of King David I of Scotland.

William of St. Barbara, the rightly elected Bishop, was forced to retreat to, and fortify, the church after his abortive entry into Durham was beaten back by Cumin's men.

In 1180 Bishop Puiset extended the church to reflect its role at the centre of a growing parish, adding the chancel.

[3] John Heath, the Elizabethan owner of the Kepier estates, Gilesgate and Old Durham is buried in the church.

St Giles Church retains some of Flambard's original building (primarily the north wall) and most of Puiset's additions.