The South Transept, also known as The Boyle Chapel, is a spartan Tudor chantry chapel, which houses the impressive monument of Sir Richard Boyle, Earl of Cork.

The tomb shows him with his first and second wives and their children, including the infant Robert Boyle, the establisher of 'Boyles Law'. Here also one can find the tomb capped with the effigies of the original founder of the chapel, Richard Benett and his wife Ellis Barry. The Villiers Heraldic Banner overhangs the tomb of Sir Edward Villiers, Lord President of Munster and half-Brother to the Duke of Buckingham. Evidence of the chapel's earlier use can be seen from the stoop at the entrance, which dates from the thirteenth century.