It seems likely that the pillars were strengthened, possibly at the beginning or middle of the 14th century.  It has been suggested that the existing remains or foundations show that a tower over the crossing was built or contemplated from the first, but it was certainly not built at the foundation. The tower held six bells weighing 47 cwt, which were unsold at the suppression. Legend says that one or two went to Lincoln Cathedral, but there is no foundation for this. Neither is it likely, in spite of rumours, that the tenor bell in All Saints’ Church, Derby came from St Mary’s Abbey, since it alone weighs 32 hundredweight, and the total weight of all six St Mary’s bells was 47 hundredweight. Three bells traditionally said to be from St Mary’s Abbey can be found in Radbourn church: one of them has the inscription ‘Jesus be our speed 1595’, which is more than half a century after St Mary’s Abbey ceased to function.

In the excavation of 1878, ribs and chamfered shafts of the tower were found, and when the excavators were cutting a drain across the tower area, many interments were met with, in each case without a coffin.  

With our backs to the ‘arch’, let us turn left into the south transept of the church. This was 25 foot six inches wide. Its east wall had two arched doorways, one into St Margaret's Chapel, one into St Werburgh's Chapel. The pier between these two doorways had the Holy Rood altar, variously described by the experts as the laiety's altar and a chantry altar within a parclose. The transept also had a door in the south east angle descending by two or three steps into an oblong room, divided into two by a wall (the sacristy – see later), and one on the west into the cloisters under the night stair. This last doorway is shown on Buck's sketch (1727) as being surmounted with a segmental arch.

A stone night stair was found, as at Torre Abbey, Bristol Abbey, Hexham Abbey and all Cistercian houses. Just the bottom two steps survive.
Let us turn left through that first doorway into St Margaret’s Chapel, and again, begin at the east end. It appears that the chapel was not part of the original design, but an extension of the earlier south transept chapels. It measures 71 feet by 16 foot six inches. The chapel was built around 1333, and its east window was a bit later than the chancel east window, and graceful, with vesicas instead of circles. A handsome keystone bearing a shield was found at the east end, also vaulting ribs and several very fine specimens of Early English carving (the bases of the arcade foundations are said to be Norman). The chapel had an altar with an alabaster reredos behind; the stone base of the altar was attached to the east wall.