Mahoney belonged to the Irish Province of the Order of Friars Minor and spent some of 1676 at Saint Isidore's College in Rome, headquarters of the province in exile. Attempting to return to Ireland from the continent where he had been ordained to priesthood, he was shipwrecked and landed in Wales. He was arrested in 1678 and imprisoned at Denbigh. He went on trial the following year at Ruthin in northern Wales where he was condemned and hanged.
An Account of the words spoken by Mr. Charles Mahoney, an Irish Priest of the holy Order of St. Francis, who was Executed in his Habit at Ruthin in North Wales, August 12, 1679. Now God Almighty is pleased I should suffer Martyrdom, his Holy Name be praised, since I dye for my Religion. But you have no Right to put me to death in this Country, though I confessed myself to be a Priest, for you seized me as I was going to my Native Country Ireland, being driven at Sea on this Coast, for I never used my Function in England before I was taken, however God forgive you, as I do and shall always pray for you, especially for those that were so good to me in my distress, I pray God bless our King, and defend him from his Enemies, and convert him to the Holy Catholick Faith, Amen. His Age was under Forty, He was tryed and Condemned at Denby [i.e. Denbigh] Confessing himself to be a Priest.