Nikephoros’s rule is endangered by Bardanes Tourkos, one of his ablest generals, who revolts and receives support from other commanders, notably the later emperors Leo V the Armenian and Michael II the Amorian in 803.

Nikephoros gains over the latter two, however, and by inducing the rebel army to disperse achieves the submission of Bardanes, who is relegated to a monastery and blinded there.

A conspiracy headed by the patrician Arsaber has a similar result.

The deposition of Empress Irene and subsequent accession of Nikephoros I signals a more violent phase in the long history of the Arab–Byzantine Wars.

Following a series of destructive annual raids across Asia Minor by the Caliphate, Irene seems to have secured a truce with Harun al-Rashid in 798 in exchange for the annual payment of tribute, repeating the terms agreed for a three-year truce following Harun's first large-scale campaign in 782.

Nikephoros, on the other hand, is more warlike and determined to refill the imperial treasury by, among other measures, ceasing the tribute.

Harun retaliates at once, launching a raid under his son al-Qasim.

Nikephoros cannot respond to this facing the ultimately unsuccessful revolt of the Asian army under Bardanes Tourkos.

After disposing of Bardanes, Nikephoros assembles his army and marches out himself to meet a second, larger invasion under the Caliph himself.

After Harun raids the frontier region, the two armies confront each other for two months in central Asia Minor, but it does not come to a battle; Nikephoros and Harun exchange etter until the Emperor arranges for a withdrawal and a truce for the remainder of the year in exchange for a one-off payment of tribute.

Nikephoros embarks on a general reorganization of the Empire, creating new themes in the Balkans and strengthening the frontiers.

Needing large sums to increase his military forces, he sets himself with great energy to increase the Empire's revenue, reimposing the taxes that Irene had remitted, and instituting other reforms that provide some insight into the financial administration of the empire during the early ninth century.

By his rigorous tax imposts he alienates the favor of his subjects, and especially of the clergy, whom he otherwise seeks to control firmly.

Although he appoints an iconodule, Nikephoros, as patriarch, Emperor Nikephoros is portrayed as a villain by ecclesiastical historians like Theophanes the Confessor.

He crowns his son Staurakios co-emperor in December 803.

In the same year, Nikephoros concludes a treaty, called the "Pax Nicephori", with Charles I of the Franks, but refuses to recognize the latter's imperial dignity.