The East Roman Empire, crippled by ineffective leadership, manages to retain Anatolia, but loses Africa to the Muslim Arabs and their newly converted Berber allies.

The Emperor's bloody persecution of the Manichaeans and suppression of popular traditions of non-Orthodox origin has meanwhile caused dissension within the Church.

In 692, Justinian convenes the so-called Quinisext Council at Constantinople to to issue disciplinary decrees related to the second and third councils of Constantinople (held in 553 and 680-681).

Also called the Council in Trullo (after the palace hall in Constantinople where it meets), the Council expands and clarifies the rulings of the Fifth and Sixth ecumenical councils (hence the name Quinisext), but by highlighting differences between the Eastern and Western observances (such as the marriage of priests and the Roman practice of fasting on Saturdays), the council compromises imperial relations with the Roman Church.

The two ecumenical councils had dealt only with doctrinal matters.

The Quinisext Council, which officially accepts as normative the decretal letters of twelve Fathers of the Church, prepares 102 canons, many of which are directed against Western Church customs and legislation.

In collections called “Nomocanons,” the council also includes, with canons of councils, imperial laws having to do with church affairs.

The Western Church and the Pope are not represented at the council.

Justinian, however, wants the Pope as well as the Eastern bishops to sign the canons.

The emperor orders Pope Sergius I arrested, but the militias of Rome and Ravenna rebel and take the Pope's side.

The Quinisext Council lays the foundation for Orthodox Canon Law, but the canons will never be fully accepted by the Western Church.

Justinian, emboldened by the increase of his forces in Asia Minor, now renews the war against the Arabs, provoking them into attacking the eastern frontier over a disagreement concerning Cypriot policy.

The Umayyad army is led by Muhammad ibn Marwan, brother of the Caliph, and included the minister of defense, the famously known Al-Hajjaj ibn Yusuf.

The imperial forcers are led by Leontios and include a "special army" of thirty thousand resettled Slavs under their leader Neboulos.

Justinian’s new troops help him to win a battle against the Caliphate in Armenia in 691, but they are soon bribed to revolt by the Arabs.

The Umayyads, incensed at the breaking of the treaty, use copies of its texts in the place of a flag.

Although the battle seems to be tilting to the imperial advantage, the defection of upwards of twenty thousand Slavs ensures a Roman defeat.

Justinian takes out his frustration, according to Theophanes, by slaughtering as many of the Slavs in and around the Opsikion Theme as he can lay his hands on, including women and children, yet modern scholars do not consider this a reliable account.

A second Arab army, commanded by Sass'n ibn an-Nu'min, is dispatched from Egypt in 693.

It faces stiff resistance in the eastern Aurés Mountains from the Jaw'ra Berbers under the command of a Jewish woman whom the Arabs refer to as Kihinah (”the Priestess”).

Soldiers of the pagan Berber tribes swell her Judeo-Berber army after the death of Kusaila.

Campaigns against the Kharajites begin to prove successful  only after 'Abd al-Malik appoints al-Hajjaj to govern Basra, but …

…another Kharijite trouble center develops north of Kufah.

Justinian II has contributed to the development of the thematic organization of the Empire, creating a new theme of Hellas in southern Greece and numbering the heads of the five major themes—Thrace in Europe, Opsikion, the Anatolikon, and Armeniakon themes in Asia Minor, and the maritime corps of the Karabisianoi—among the senior administrators of the Empire.

He has also sought to protect the rights of peasant freeholders, who serve as the main recruitment pool for the armed forces of the Empire, against attempts by the aristocracy to acquire their land—putting him in direct conflict with some of the largest landholders in the Empire.

Although strife between Blues and Greens has persisted throughout the century, internal revolt has failed to imperil the Heraclian dynasty until the reign of Justinian II.

If his land policies threaten the aristocracy, his tax policy is no more popular with the common people.

Through his ruthless policy and the merciless extortion by his finance officials Stephen and Theodotos, the emperor has raised the funds to gratify his sumptuous tastes and his mania for erecting costly buildings.

This, ongoing religious discontent, conflicts with the aristocracy, and displeasure over his resettlement policy eventually drives his subjects into rebellion.

The population rises in 695 under Leontios, the strategos of Hellas, imprisoned by the emperor after the defeat by the Arabs at Sebastopolis and newly freed, and proclaims him Emperor.

Justinian is deposed and his nose is cut off (it will later be replaced by a solid gold replica of his original) to prevent his again seeking the throne: such mutilation is common in the of the Eastern Roman Empire (hence his byname Rhinotmetus).

He is exiled to Cherson in the Crimea.

A patrician by the name of Symbatius had proceeded to rebel in Armenia in the meantime, and opened up the province to the Arabs, who proceed to conquer it in 694–695.

Abd al-Malik had also resumed campaigns against the Empire in Anatolia in 692, but no permanent conquest ensues.

These campaigns are partly designed to keep the Syrian troops fit.