On the death of his father, Constantine IV, in September 685, Justinian II became emperor at the age of 16. At the beginning of his reign he made a treaty with the Arabs whereby they paid increased tribute and agreed to joint sovereignty over Cyprus, Armenia, and Georgia. In 688/689 he led a successful expedition into Slav-occupied territory in Thrace and Macedonia, and many Slavs were drafted into the Byzantine army or settled as soldier-farmers in Asia Minor. Disagreement over Cypriot policy, however, provoked the Arabs into attacking the eastern frontier. In 691–692 they defeated the Byzantines at Sebastopolis and conquered Byzantium's Armenian possessions.

At home Justinian held the Quinisext Council, the disciplinary rulings of which were intended to supplement the doctrinal canons of the fifth and sixth ecumenical councils. Pope Sergius I's refusal to recognize them led to friction between him and Justinian.

The emperor's ruthless policy and the merciless extortion by his finance officials led to a revolt in 695 in which a new emperor was proclaimed. Justinian's nose was cut off (hence his byname Rhinotmetus), and he was banished to Cherson on the Crimean peninsula. Several years later, on learning that Emperor Tiberius III Apsimar planned to arrest him, he escaped to the khan of the Khazars (Khazar), with whom the Heraclians had close ties of friendship. Shortly after Justinian's marriage to the khan's sister, however, the khan was bribed by the Byzantine emperor to kill Justinian. Forewarned by his wife, Justinian fled to the Bulgar kingdom. Gaining the help of their khan and his army, Justinian marched on Constantinople, captured the city, and was once more acclaimed emperor (705).

Justinian's second reign was marked by a reconciliation with the papacy, cemented by Pope Constantine's visit to Constantinople (710–711). The emperor was obsessed, however, with a desire for revenge against his opponents, and the resulting mass executions in turn led to the alienation of many of his former supporters. In 711 a revolt, aided by the Khazars, broke out in Cherson. An Armenian, Bardanes (who ruled as Philippicus), was proclaimed emperor, sailed to Constantinople, and took possession of the city. Justinian and his family were killed.