The Chapel was built and dedicated to St Bernard of Clairvaux in 1530 when, what is now the Front Quad of St John's was St Bernard's College: the house of studies in Oxford for young Cistercian monks. The Chapel was re-dedicated to St John the Baptist in 1557, when the first members of the new St John Baptist College came into residence.
The interior has undergone a number of changes over the centuries, notably a complete re-ordering in 1840 which created the gothic revival pews, roof, wall arcading and west screen that you see today. A book with translations of Latin inscriptions can be found in the sanctuary to the south of the main altar.
The small Baylie chapel in the north-east corner, which forms a more intimate space for daily prayers, was added in the late C17th and has a late fan-vaulted ceiling. Many monuments that originally stood elsewhere have been moved into this small chapel. A notable recent feature is the modern Coptic icon of the Baptism of Jesus by John the Baptist, made in Egypt for St John's Chapel. Opposite the entrance to the Baylie Chapel, on the south wall of the main sanctuary, is a modern triptych of the life of St John, by the contemporary artist Nicholas Mynheer.
Until the 1930s, what is now the passage outside Chapel was its narthex. In the C17th a carved wooden screen separated the narthex from the west end of the Chapel. Nothing remains of the C17th screen save some pillars now in Painswick House in Gloucestershire. William Laud, President of St John's 1611-21 - who later became Archbishop of Canterbury, was executed in 1645 during the struggles between King and Parliament, and was reburied under the Chapel altar in 1663 - placed carved altar rails before the altar, but these were also removed during the Victorian alterations and can now be seen in Northmoor Church near Oxford. Laud donated the Chapel's first organ, a large and expensive one which stood on the north wall near the altar but was dismantled not long after his death. The next time a notable organ arrived in St John's was in 2008, when the organ by Bernard Aubertin replaced a series of organs in the west gallery.