Nikephoros came into conflict with Emperor Michael in 1078 when he pleaded with the emperor to address the worsening situation in Byzantine Anatolia, insulting Michael with his frankness. In order to protect himself, Nikephoros gathered an army of native troops and Turkish mercenaries and declared himself emperor in July or October 1077. Nikephoros gathered a strong support base due to his military acumen and family renown and was later recognized by the Byzantine Senate on 7 January 1078, after which he seized the throne with the help of the citizens of Constantinople.

As emperor, Nikephoros faced numerous revolts, including those of Nikephoros Bryennios, Nikephoros Basilakes, and Constantine Doukas, as well as an attempted assassination by the Varangian Guard. Nikephoros embraced the trappings of an emperor, performing many acts to increase his legitimacy and support, such as spending large amounts on donatives for the army and his supporters, forgiving all debt in arrears, and instituting minor legal reforms. Diplomatically, Nikephoros secured the submission of Theodore Gabras and Philaretos Brachamios, governors of Trebizond and Antioch, respectively, who had become de facto independent of the Byzantine Empire due to the constant incursions of the Seljuks into Byzantine Anatolia.