The stained glass windows in the Cathedral are both distinctive and beautifully crafted. All the clerestory windows are by Grosse de Herde, a renowned Belgium company, which also supplied windows during the second stage of the Cathedral’s development. The smaller windows at the back of the nave on the northern and southern sides are of enamelled glass.

The window depicting the Transfiguration of Jesus in the southern transept was donated by Bishop Lanigan. The window above the altar on the eastern front,  donated by Mrs. Dalglish, was by John Hardman and Company. Several of the windows are in need of repair as part of the conservation works.