At the back of the church, two beautifully painted windows flank the baptistry, representing St Paul (South) and St Barnabas (North). These windows demonstrate the genius of T R Spence: at first glance they appear to be fine examples of gothic design, but on closer inspection one sees the gentle introduction of art nouveau at the base of each window, and at the top the designs first noted on the entrance gates are repeated in a different form. Other examples of this unity of design can be found in other parts of the building, notably the East window, the lectern and the south windows. 

The flat roofed Baptistry provides an ideal setting for the font of Mexican onyx, standing on rouge jasper columns on a base of alabaster. Originally there existed a beautiful iron and copperwork font cover in the style of the entrance gates, but unfortunately this disappeared without trace many years ago. The ceilings of the nave have already been noted; in the baptistry is another painted ceiling of an entirely different design. 

The mosaic floor of the baptistry contains the fish symbol used from early Christian times to denote the name of Jesus. In the baptistry windows can be seen other symbols: from left to right, a crown and olive branch, a peacock, three fish, a dove with an olive branch, a shield with a lily and an anchor and lamp. 

On the west wall above the Baptistry is a fine tracery screen worked in Caen stone installed in November 1890. This was significantly redesigned in the summer of 1889 and was probably not part of the original intention, which was perhaps to decorate all the upper walls in colour. As Mitchell’s attention was shifting to Aberdeen, and the University extension scheme at Marischall College, this screen in a sense signalled closure on the building project at Jesmond.

The west window of the Last Judgement is by J W Brown of London.