The church of St Mary Magdalen appears in records as early as 1260, was rebuilt in 1308, was destroyed in 1316, and yet its precise position on the ground remains unidentified. A place can leave a clear paper trail and still manage to disappear entirely.

The broader complex to which the chapel belonged, known as St John's Priory and Hospital or sometimes as "Palmer's hospital", was founded between 1185 and 1188 by a man named Ailred the Palmer. Ailred and his wife took monastic vows alongside a group of fellow workers, who formed a community of brothers and sisters dedicated to caring for the poor and infirm. Unusually for the period, the sisters appear to have had a genuine role in managing the institution, as the hospital's own register makes clear. In 1308, John Decer, who was then mayor of Dublin, added a chapel of St Mary within the hospital precinct. That chapel stood for barely eight years. In 1316, as the forces of Edward Bruce advanced on the city during the Bruce invasion of Ireland, Dublin's citizens set fire to the Thomas Street suburbs themselves to deny the approaching army shelter and resources. The church of St John and the chapel of St Magdalen both burned in that act of scorched-earth defence. A will from 1388, that of a man named John Hamound, records a bequest to the church of St Mary Magdalen for masses and wax, and asks that he be buried before its door in the cemetery of St John, outside the New Gate, which was one of the principal gates in the medieval city wall. Whether the church had been rebuilt by then, or whether Hamound was bequeathing to a memory, the document does not clarify.

The site today is occupied by the Augustinian friary of St John on Thomas Street, with the relevant area extending into the buildings to the east and west of the friary. There is nothing to mark the chapel specifically, and given that its location has not been archaeologically confirmed, a visit is less about seeing something and more about standing in the approximate vicinity of something lost. The friary itself is a working religious house. The interest here is in the layering, a medieval hospital founded by a palmer (a pilgrim who had returned from the Holy Land), a mayor's chapel, a deliberate burning, a merchant's will, and a site that scholarship has circled for decades without being able to fix to a single spot.