The future al-Mutawakkil was born on February/March 822 to the Abbasid prince Abu Ishaq Muhammad (the future al-Mu'tasim) and a slave concubine from Khwarazm called Shuja. His early life is obscure, as he played no role in political affairs until the death of his older half-brother, al-Wathiq, in August 847.
Al-Wathiq's death was unexpected, and although he had a young son, he had not designated a successor. Consequently the leading officials,the vizier Muhammad ibn al-Zayyat, the chief qādī, Ahmad ibn Abi Duwad, the Turkish generals Itakh and Wasif al-Turki, and a few others, assembled to determine his successor. Ibn al-Zayyat initially proposed al-Wathiq's son Muhammad (the future al-Muhtadi), but due to his youth he was passed over, and instead the council chose the 26-year-old Ja'far, who became the caliph al-Mutawakkil. The officials obviously hoped that the new Caliph would prove a pliable puppet, like al-Wathiq. In this they made a fatal miscalculation, for al-Mutawakkil was resolved to restore the authority of the caliphal office and restore its independence by destroying the coterie of civil and military officials, raised by his father, that effectively controlled the state.
Al-Mutawakkil's first target was the vizier Ibn al-Zayyat, against whom he harboured a deep grudge over the way he had disrespected him in the past. According to al-Tabari, when al-Wathiq had grown angry and suspicious at his brother, al-Mutawakkil had visited the vizier in hopes of persuading him to intercede with the Caliph. Not only had Ibn al-Zayyat kept the Abbasid prince waiting until he finished going through his correspondence, but even mocked him, in the presence of others, for coming to him seeking assistance. Not only that, but when the dejected prince left, Ibn al-Zayyat wrote to the Caliph to complain about his appearance, noting that he was dressed in effeminate fashion, and that his hair was too long. As a result, al-Wathiq had his brother summoned to court. Al-Mutawakkil came in a brand-new court dress, hoping to mollify the Caliph, but instead al-Wathiq ordered that his hair be shorn off, and al-Mutawakkil be struck in the face with it. In later times, al-Mutawakkil confessed that he had never been so distressed by anything in his life than by this public humiliation. Thus, on 22 September 847, he sent Itakh to summon Ibn al-Zayyat as if for an audience. Instead, the vizier was brought to Itakh's residence, where he was placed under house arrest. His possessions were confiscated, and he was tortured to death.
This was the apogee of Itakh's career: he combined the positions of chamberlain (ḥājib), head of the Caliph's personal guard, intendant of the palace, and head of the barīd, the public post, which doubled as the government's intelligence network. In 848, however, he was persuaded to go to the pilgrimage, and laid down his powers, only to be arrested on his return. His possessions were confiscated—reportedly, in his house alone the Caliph's agents found one million gold dinars. He died of thirst in prison on 21 December 849.
One Mahmud ibn al-Faraj al-Nayshapuri arose claiming to be a prophet. He and some followers were arrested in Baghdad. He was imprisoned, beaten and on June 18, 850 he died.
In A.H. 236 (850) al-Mutawakkil issued a decree requiring all Christians and Jews in his realm including Jerusalem and Caesarea to wear a yellow (honey-colored) hood and belt to distinguish them from Muslims.
In A.H. 237 (851–852) Armenians rebelled and defeated and killed the Abbasid governor. Al-Mutawakkil sent his general Bugha al-Kabir to handle this. Bugha scored successes this year and the following year he attacked and burned Tiflis, capturing Ishaq ibn Isma'il. The rebel leader was executed. That year (A.H. 238) the Byzantines attacked Damietta.
In A.H. 240 (854–855) the police chief in Homs killed a prominent person stirring an uprising. He was driven out. Al-Mutawakkil offered another police chief. When the next year saw a revolt against this new police chief, al-Mutawakkil had this firmly suppressed. As Christians had joined in the second round of disturbances, the caliph had Christians expelled from Homs.
Also in 241 occurred the firm response to the revolt by the Bujah, people of descent just beyond Upper Egypt. They had been paying a tax on their gold mines. They ceased paying this, drove out Muslims working in the mines and terrified people in Upper Egypt. Al-Mutawakkil sent al-Qummi to restore order. Al-Qummi sent seven ships with supplies that enabled him to persevere despite the very harsh terrain of this distant territory. He retook the mines, pressed on to the Bujah royal stronghold and defeated the king in battle. The Bujah resumed payment of the tax.
On February 23, 856, there was an exchange of captives with the Byzantines. A second such exchange took place some four years later.
Al-Mutawakkil's reign is remembered for its many reforms and viewed as a golden age of the Abbasids. He would be the last great Abbasid caliph; after his death the dynasty would fall into a decline.
Al-Mutawakkil continued to rely on Turkish statesmen and slave soldiers to put down rebellions and lead battles against foreign empires, notably the Byzantines, from whom Sicily was captured. His secretary, Al-Fath ibn Khaqan, who was Turkish, was a famous figure of Al-Mutawakkil's era. His reliance on Turkish soldiers would come back to haunt him. Al-Mutawakkil would have his Turkish commander-in-chief killed. This, coupled with his extreme attitudes towards the Shia, made his popularity decline rapidly.
Al-Mutawakkil had appointed his oldest son, al-Muntasir, as his heir in 849/50, but slowly had shifted his favour to his second son, al-Mu'tazz, encouraged by al-Fath ibn Khaqan and the vizier Ubayd Allah ibn Yahya ibn Khaqan. This rivalry extended into the political sphere, as al-Mu'tazz's succession appears to have been backed by the traditional Abbasid elites as well, while al-Muntasir was backed by the Turkish and Maghariba guard troops. In late autumn 861, matters came to a head: in October, al-Mutawakkil ordered the estates of the Turkish general Wasif to be confiscated and handed over to al-Fath. Feeling backed into a corner, the Turkish leadership began a plot to assassinate the Caliph. They were soon joined, or at least had the tacit approval, of al-Mustansir, who smarted from a succession of humiliations: on 5 December, on the recommendation of al-Fath and Ubayd Allah, he was bypassed in favour of al-Mu'tazz for leading the Friday prayer at the end of Ramadan, while three days later, when al-Mutawakkil was feeling ill and chose al-Mustansir to represent him on the prayer, once again Ubayd Allah intervened and persuaded the Caliph to go in person. Even worse, according to al-Tabari, on the next day al-Mutawakkil alternately vilified and threatened to kill his eldest son, and even had al-Fath slap him on the face. With rumours circulating that Wasif and the other Turkish leaders would be rounded up and executed on 12 December, the conspirators decided to act.
According to al-Tabari, a story later circulated that al-Fath and Ubayd Allah were forewarned of the plot by a Turkish woman, but had disregarded it, confident that no-one would dare carry it out. On the night of 10/11 December, about one hour after midnight, the Turks burst in the chamber where the Caliph and al-Fath were having supper. Al-Fath was killed trying to protect the Caliph, who was killed next. Al-Muntasir, who now assumed the caliphate, initially claimed that al-Fath had murdered his father, and that he had been killed after; within a short time, however, the official story changed to al-Mutawakkil choking on his wine. The murder of al-Mutawakkil began the tumultuous period known as "Anarchy at Samarra", which lasted until 870 and brought the Abbasid Caliphate to the brink of collapse.
In 850 Mutawakkil made a decree ordering Dhimmi (Jews) wear garments to distinguish them from Muslims, their places of worship destroyed, demonic effigies nailed to the door, and that they be allowed little involvement government or official matters.
Mutawakkil ordered the ancient sacred Cypress of the Zoroastrians, Cypress of Kashmar to be cut down in order to use it in constructing his new palace despite the enormous protests from the Zoroastrian community. The cypress was of legendary values to the Zoroastrians, believed to be brought from Paradise to the earth by Zoroaster was more than 1400 years old at the time. He was killed before the cypress wood arrived for his new palace.
Al-Mutawakkil was unlike his brother and father in that he was not known for having a thirst for knowledge, but he had an eye for magnificence and a hunger to build. The Great Mosque of Samarra was at its time, the largest mosque in the world; its minaret is a vast spiralling cone 55 m high with a spiral ramp. The mosque had 17 aisles and its wall were panelled with mosaics of dark blue glass.
The Great Mosque was just part of an extension of Samarra eastwards that built upon part of the walled royal hunting park. Al-Mutawakkil built as many as 20 palaces (the numbers vary in documents). Samarra became one of the largest cities of the ancient world; even the archaeological site of its ruins is one of the world's most extensive. The Caliph's building schemes extended in A.H. 245 (859–860) to a new city, al-Jaʻfariyya, which al-Mutawakkil built on the Tigris some eighteen kilometres from Samarra. More water, and al-Mutawakkil ordered a canal to be built to divert water from the Tigris, entrusting the project to two courtiers, who ignored the talents of a local engineer of repute and entrusted the work to al-Farghanī, the great astronomer and writer. Al-Farghanī, who was not a specialist in public works, made a miscalculation and it appeared that the opening of the canal was too deep so that water from the river would only flow at near full flood.
News leaked to the infuriated caliph might have meant the heads of all concerned save for the gracious actions of the engineer, Sind ibn ʻAlī, who vouched for the eventual success of the project, thus risking his own life. Al-Mutawakkil was assassinated shortly before the error became public.
Al-Mutawakkil was keen to involve himself in many religious debates, something that would show in his actions against different minorities. His father had tolerated the Shīʻa Imām who taught and preached at Medina, and for the first years of his reign al-Mutawakkil continued the policy. Imām ʻAlī al-Hadī's growing reputation inspired a letter from the Governor of Medina, ʻAbdu l-Lāh ibn Muħammad, suggesting that a coup was being plotted, and al-Mutawakkil extended an invitation to Samarra to the Imām, an offer he could not refuse. In Samarra, the Imām was kept under virtuial house arrest and spied upon. However, no excuse to take action against him ever appeared. After al-Mutawakkil's death, his successor had the Imām poisoned: al-Hadī is buried at Samarra. The general Shīʻa population faced repression. and this was embodied in the destruction of the shrine of Hussayn ibn ʻAlī, an action that was carried out ostensibly in order to stop pilgrimages to that site, and the flogging and incarceration of the Alid Yahya ibn Umar.
Also during his reign, Al-Mutawakkil met the famous Byzantine theologian Cyril the Philosopher, who was sent to tighten the diplomatic relations between the Empire and the Caliphate in a state mission by the Emperor Michael III. Of his sons, al-Muntasir succeeded him and ruled until his death in 862, al-Mu'tazz reigned as Caliph from 866 to his overthrow in 869, and al-Mu'tamid reigned as Caliph in 870–892 with his brother al-Muwaffaq serving as an effective regent of the realm until his death in 891.