During his minority, the empire was governed by his mother Theodora, who in spite of several defeats inflicted upon her generals maintained the frontiers against the Saracens of Baghdad and Crete. The regent displayed her religious zeal by restoring veneration of icons in 842 and persecuting the Paulician heretics, but she entirely neglected the education of her son. As a result, Michael reportedly grew up a debauchee, and fell under the sway of his uncle Bardas, who induced him to banish Theodora to a convent and practically assumed the chief control in 857.
Bardas justified this usurpation by introducing various internal reforms; in the wars of the period Michael himself took a more active part. During a conflict with the Saracens of the Euphrates (856 - 863), the emperor sustained a personal defeat in 860, which was retrieved by a great victory on the part of his uncle Petronas in Asia Minor.
Emperor Michael III under the guidance of Patriarch Photius I, sent, in 860, the Saints Cyril and Methodius as envoys to the Khazar Khagan in an effort to stop the expansion of Judaism in the Khazar tribe. This mission was a failure.
In 861 Michael and Bardas invaded Bulgaria and secured the conversion of the king to Christianity. On the sea the empire suffered under the ravages of the Cretan corsairs; and in 865 the first pillaging expedition of the Rus' endangered the Bosporus. In 862 Cyril and Methodius were sent to Great Moravia to a new missionary expedition to expand the Eastern Christianity faith.
In 867, Michael was assassinated by Basil the Macedonian, a former groom, who had overthrown the influence of Bardas and in 866 been elevated by Michael to the highest posts in the government, even marrying Michael's favorite mistress, Eudocia Ingerina. Michael's unflattering reputation in later centuries was largely a result of Basil's propaganda, which sought to justify his usurpation of power.