British History Online states:
The church of St. John Baptist, commonly called St. John Zachary, is first mentioned in the taxation of 1217. It stood on the west side of Milne Street and served a parish originally containing many dwelling-houses which were gradually taken over by religious houses and University hostels, which, in their turn, were destroyed to make room for King’s College. The site of its east end is today covered by the western bays of King’s College Chapel. Besides being the parish church it served as a chapel for the scholars of Clare Hall and of Trinity Hall. In 1445 Henry VI acquired both the church and the churchyard, along with the adjoining lands. The church was probably destroyed soon after 25 July 1446, when the first stone of King’s College Chapel was laid. By 1453 it had been rebuilt at the charges of Henry VI at the north-west corner of the Old Court of King’s College, on a site now occupied in part by the departmental libraries of the University. This second edifice is last mentioned in 1488–9; it was presumably allowed to fall into decay since by that time the parish no longer existed, and its site was used for King’s College buildings.
The site is marked on the map on Susanna Gregory’s website.
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