The Council settled a set of theological controversies that go back to the sixth century but had intensified under the Emperors
Heraclius (610–641) and
Constans II (641–668). Heraclius had set out to recover much of the part of his Empire lost to the Persians and had attempted to bridge the controversy with
Monophysitism, which was particularly strong in Syria and Egypt, by proposing a moderate theological position that had as good support in the tradition as any other. The result was first
monoenergism, i.e. that Christ, though existing in two natures, had one energy (divine and human), the second was
monothelitism, i.e. that Christ had one will (that is, that there was no opposition in Christ between his human and divine volition). This doctrine was accepted in most of the Byzantine world, but was opposed at Jerusalem and at Rome and started a controversy that persisted even after the loss of the reconquered provinces and the death of Heraclius. When Heraclius' grandson Constans II took the throne, he saw the controversy as threatening the stability of the Empire and attempted to silence discussion, by outlawing speaking either in favour or against the doctrine.
Pope Martin I and the monk
Maximus, the foremost opponents of monothelitism (which they interpreted as denying a human faculty of will to Christ), held a
synod in Rome in 649 that condemned monoenergism and monothelitism.
 At Constantinople some accused the Pope of supporting revolution, this was regarded as high treason, and Martin and Maximus were accordingly arrested, tried, condemned and sent into exile, where the Pope soon died.
After Constans' son and successor,
Constantine IV had overcome the Muslim siege of Constantinople in 678, he immediately set his sights on restoring communion with Rome: he wrote to
Pope Donus suggesting a conference on the matter. When the letter reached Rome, Donus had died, but his successor,
Pope Agatho, agreed to the Emperor's suggestion and ordered councils held throughout the West so that legates could present the tradition of the Western Church. Then he sent a delegation to meet the Easterners at Constantinople.
 In the meantime, Constantine summoned
Patriarch George I of Constantinople and all bishops of his jurisdiction of
Constantinople to a council. He also summoned
Patriarch Macarius of Antioch, a Byzantine appointee permanently resident in Constantinople because of the Muslim occupation of his see.