He was educated in Sicily then ordained priest at Rome.
He had been put forward as a compromise candidate, there being a conflict between the two factions resident in Rome—military and clerical. On his death, Conon was buried in the Patriarchal Basilica of Saint Peter. He may have been among the many Sicilian clergy in Rome, at that time, due to the Islamic Caliphate attacks on Sicily in the mid-7th century.
His age, venerable appearance, and simple character caused the clergy and soldiery of Rome, who were in disagreement, to put aside their respective candidates and to elect him as pope.
He was consecrated on 21 October 686 after notice of his election had been sent to the Exarch of Ravenna, or after it had been confirmed by him. (Vita South Kiliani, in Canisius, Lecturer Antiquæ, III, 175–180) He was in favour with Byzantine Emperor Justinian II, who informed him that he had recovered the Acts of the Third Council of Constantinople, by which, the Emperor wrote, it was his intention to abide.
Justinian also remitted certain taxes and dues owing to the imperial exchequer from several papal patrimonies.