It was added in the mid fifteenth century by Archbishop Richard O'Hedian, and its insertion appears to have compressed the nave into an unusually short space, just fifteen metres long. Between 1504 and 1525, a second floor was built over that nave, connecting to the tower house and seemingly functioning as an upper hall, a domestic arrangement grafted onto a liturgical one in a way that says a good deal about how ecclesiastical authority was exercised in late medieval Ireland.

The cathedral is cruciform in plan, built from limestone rubble set in rough courses, and its construction was spread across several centuries. The choir, the oldest surviving phase, dates to the 1230s and is distinguished by the fact that all its carved stonework is sandstone rather than limestone, a material contrast still visible today. Lancet windows line the choir walls, with unusual clerestorey quatrefoils set into segmental-arched embrasures with curving sills above them. The 15th-century crossing tower, where nave and choir intersect, rests on four 13th-century clustered columns with ornate limestone capitals. Its ribbed vault was largely rebuilt in 1875, reportedly because the original had been damaged when the bells were moved during the siege of 1647. Sculpted corbels inside the tower carry animal and human heads, and ogee-headed windows, their curves characteristic of late Gothic taste, admit what light there is. Tucked beneath the spiral staircase in the north-west pier of the crossing is a rock-cut well, predating the cathedral entirely. The south transept retains a recently restored wall painting of the crucifixion, while the chapels off the corresponding north transept project outward from the body of the building, gabled and twin-lit. The chapels in the south transept, dedicated to St Brigid and the Blessed Virgin, are not projections at all but spaces carved directly out of the wall thickness.

The cathedral also contains a tomb recess in the choir's south wall holding the effigy of Archbishop Miler Magrath, and the majority of the altar tombs and wall memorials throughout the building date from the 16th century. Running through the walls of both transepts are mural passages, narrow corridors built within the masonry itself, accessible by winding staircases and connected by steep internal flights that extend over the eastern tower arch and into the nave walls. It is the kind of detail easily missed from the floor, but worth looking for: an entire circulatory system hidden inside the stone.