St Michael's Loft, built over the Lady Chapel in the 15th century, was the last part of the fabric of the church to be completed. It is a consecrated chapel dedicated to St Michael, but the original use for which it was intended is not really known. That remains one of the medieval mysteries of the Priory.

The altar, piscina and corbels at the eastern end of the chapel suggest its definite use as a chapel, and it may be that the original intention was that it should be used as a training chapel for the oblates and noviciates coming into the Augustinian Order. The Augustinians at Christchurch were, from the middle of the 12th century, canons regular who had to be ordained.