Chrysanthus was born Charilaos Filippidis in Komotini, Thrace in 1881. He studied at the Theological School of Chalki, furthering his studies in Leipzig and Lausanne. He became Metropolitan of Trapezus in 1913 and served in that post until 1938 when he was named Archbishop of Athens and all Greece.
When Greece capitulated in the Second World War in April 1941, Chrysanthus refused to bless the swearing-in ceremony for quisling Prime Minister Georgios Tsolakoglou. For this action, he was dethroned on July 2, 1941 and replaced by Archbishop Damaskinos.