The east bay of the chapel was vaulted, but the rest had a timber roof. The east bay had a pretty vaulted tomb with a screen, and a fine canopied tomb, white-washed. The stone coffin was missing but the leg bones ‘of a powerful man’ were found. It is surmised that this tomb was occupied by one of the founders of the Abbey, and Richard of Sandiacre, William FitzRalph or Geoffrey de Salicosa Mara have been suggested. Fragments of its canopy are preserved in the museum. At the Suppression, the tomb had a 'grate of yren'.

The chapel was separated from the chancel by three arches supported by beautiful clustered piers: their bases remain. The fourth bay had a solid wall. On the south side of the chapel, it was separated from St Werburgh's Chapel by three arches. Their octagonal pier bases remain and are very plain and elegant, in the Decorated style. It has been noted that the east respond of the arcade between St Margaret's and St Werburgh's was much earlier, and the question has been asked: was the chapel partly rebuilt in the 14th century?

Let us turn now from St Margaret’s Chapel into the neighbouring St Werburgh’s Chapel.  This also was not part of the original plan, but an extended south transept chapel. It measures 52 feet by 13 foot six inches and was apparently a rebuilding in the 14th century under William de Horsley, of a 13th century original mentioned in the charter.

Fragments of an alabaster altar table were found at the east end of the chapel as the inventory bears witness to. There were no interments by the altar, but in the south side of the chapel, however, at a depth of three feet, the skeleton of an aged man was found; there was no trace of a coffin, and the bones may have belonged to a canon of the Abbey.

St Werburgh's chapel has14th century pillar bases, but the eastern respond of the arcade is much earlier, as noted in the description of St Margaret’s Chapel. Some jiggery-pokery had to be resorted to, in order to make the old fit the new: it appears that the rebuilders built a respond on the east side of the great pier thus making the pillar 'move' as far to the east as possible. Even so, the westernmost arch of the arcade is smaller than the others. The arcade bases are Decorated.

The eastern respond of the arcade was built on part of a monumental slab with a fine incised cross fleury, very like one in the Chapter House. The pillar next to it also nearly covers an incised slab. The original excavator thought these were probably relics of the Augustinian canons, but recent opinion is that there is nothing of their building on this site. Between the easternmost pillars was a snail vault containing three skulls and several bones.