He came to the throne at the age of 13, the youngest Caliph in Abbasid history, as a result of palace intrigues. His accession was soon challenged by the supporters of the older and more experienced Abdallah ibn al-Mu'tazz, but their attempted coup in December 908 was quickly and decisively crushed. Al-Muqtadir enjoyed a longer rule than any of his predecessors, but was uninterested in government. Affairs were run by his officials, although the frequent change of viziers—fourteen changes of the head of government are recorded for his reign—hampered the effectiveness of the administration. The harem, where his mother, Shaghab, exercised total control, also exercised a frequently decisive influence on affairs, and especially on the advancement or dismissal of officials. After a period of consolidation and recovery under his father al-Mu'tadid and older half-brother al-Muktafi, al-Muqtadir's reign marks the onset of rapid decline. The full treasury inherited by al-Muqtadir was quickly emptied, and financial difficulties would become a persistent feature of the caliphal government. Ifriqiya fell to the Fatimids, although the commander-in-chief Mu'nis al-Muzaffar was able to repel their attempts to conquer Egypt as well. Nearer to Iraq, the Hamdanids became autonomous masters of the Jazira and the Qarmatians re-emerged as a major threat, culminating in their capture of Mecca in 929. The forces of the Byzantine Empire, under John Kourkouas, began a sustained offensive into the borderlands of the Thughur and Armenia. As a result, in February 929 a palace revolt briefly replaced al-Muqtadir with his brother al-Qahir. The new regime failed to consolidate itself, however, and after a few days al-Muqtadir was restored. The commander-in-chief, Mu'nis al-Muzaffar, was by then a virtual dictator. Urged by his enemies, al-Muqtadir attempted to get rid of him in 932, but Mu'nis marched with his troops on Baghdad, and in the ensuing battle on 31 October 932 al-Muqtadir was killed.
The future al-Muqtadir was born on 14 November 895, as the second son of Caliph al-Mu'tadid (r. 892–902). His mother was the Greek slave concubine Shaghab. Al-Mu'tadid was the son of al-Muwaffaq, an Abbasid prince who became the Caliphate's main military commander, and de facto regent, during the rule of his brother, al-Mu'tamid (r. 870–892). Al-Muwaffaq's power relied on his close ties with the ghilmān, the foreign-born "slave-soldiers" that now provided the professional mainstay of the Abbasid army. The ghilmān were highly proficient militarily, but also very expensive, and a potential political danger, as their first priority was securing their pay; alien to the mainstream of Muslim society, the ghilmān had no compunctions to overthrow a vizier or even a caliph to secure their aims, as demonstrated during the "Anarchy at Samarra" (861–870), when five caliphs succeeded one another.
Caliphal authority in the provinces collapsed during the "Anarchy at Samarra", with the result that by the 870s the central government had lost effective control over most of the Caliphate outside the metropolitan region of Iraq. In the west, Egypt had fallen under the control of Ahmad ibn Tulun, who also disputed control of Syria with al-Muwaffaq, while Khurasan and most of the Islamic East had been taken over by the Saffarids, who replaced the Abbasids' loyal client state, the Tahirids. Most of the Arabian peninsula was likewise lost to local potentates, while in Tabaristan a radical Zaydi Shi'a dynasty took power. Even in Iraq, the rebellion of the Zanj slaves threatened Baghdad itself, and further south the Qarmatians were a nascent threat. Until his death in 891, al-Muwaffaq was engaged in a constant struggle to avert complete collapse, but managed to suppress the Zanj and repel the Saffarids. Upon his death, his son assumed his powers, and when Caliph al-Mu'tamid died in 892, he usurped the throne from his sons. Al-Mu'tadid would prove to be the epitome of the "warrior-caliph", spending most of his reign on campaign. He managed to overthrow the local dynasts who had seized power during the Anarchy and restore control over the Jazira, the frontier towns of the Thughur, and the Jibal, but his attempts to capture Fars and Kirman were unsuccessful. In other areas, however, the fragmentation of the Islamic world continued: the Sajid dynasty was established in Adharbayjan, the Armenian princes became de facto independent, Yemen was lost to a local Zaydi dynasty, and a new radical sect, the Qarmatians, emerged and in 899 seized Bahrayn. His successor, al-Muqtadir's older half-brother al-Muktafi, was a more sedentary figure but continued al-Mu'tamid's policies, and was able to score a major victory over the Qarmatians, and reconquer the Tulunid domains.
All this came at the cost of gearing the state towards war: according to the historian Hugh N. Kennedy, based on a treasury document from the time of al-Mu'tadid's accession, "out of the total expenditure of 7915 dinars per day, some 5121 are entirely military, 1943 in areas (like riding animals and stables) which served both military and non-military and only 851 in areas like the bureaucracy and the harem which can be described as truly civilian (though even in this case, the bureaucrats’ main purpose seems to have been to arrange the payment of the army). It seems reasonable to conclude that something over 80 per cent of recorded government expenditure was devoted to maintaining the army." Paying the army thus became the chief concern of the government, but it became an increasingly difficult proposition as the outlying provinces were lost. The situation was further exacerbated by the fact that in the remaining provinces, semi-autonomous governors, grandees and members of the dynasty were able to establish virtual latifundia, aided by the system of muqāṭa'a, a form of tax farming in exchange for a fixed tribute, which they often failed to pay. Even the revenues of the Sawad, the rich agricultural lands of Iraq, are known to have declined considerably at the time. Nevertheless, through stringent economy, and despite near-constant warfare, both al-Mu'tadid and al-Muktafi were able to leave a full treasury behind. Thus the restored Caliphate at the time of al-Muktafi's death was less than half in size than in its heyday under Harun al-Rashid (r. 786–809), but it remained a powerful and viable state, with an army that, "though it was very expensive, was probably the most effective in the Muslim world", and an almost unchallenged legitimacy as the true successors of Muhammad.
In 908, al-Muktafi fell ill, and was evidently nearing his end. The issue of succession had been left open, and with the Caliph incapacitated, the vizier al-Abbas ibn al-Hasan al-Jarjara'i took it upon himself to seek out a successor. Two different versions are told of the events: Miskawayh reports that the vizier sought the advice of the most important bureaucrats (kuttāb, sing. kātib), with Mahmud ibn Dawud ibn al-Jarrah suggesting the older and experienced Abdallah ibn al-Mu'tazz, but Ali ibn al-Furat—who is usually portrayed as a villain by Miskawayh—proposing instead the thirteen-year-old Ja'far al-Muqtadir as someone weak, pliable, and easy to be manipulated by the senior officials. The vizier also consulted Ali ibn Isa al-Jarrah, who refused to choose, and Muhammad ibn Abdun, whose opinion has not been recorded. In the end, the vizier concurred with Ibn al-Furat, and on al-Muktafi's death Ja'far was proclaimed as heir and brought to the caliphal palace; when the testament of al-Muktafi was opened, he too had chosen his brother as his successor. A different story is reported by the Andalusi historian Arib, whereby the vizier dithered between the candidacies of Ibn al-Mu'tazz and another older Abbasid prince, Muhammad ibn al-Mu'tamid. The choice of the latter would represent a major political departure, in effect a repudiation of al-Mu'tadid's coup that had deprived the offspring of al-Mu'tamid of power, and of the officials and ghilmān that had underpinned al-Mu'tadid's regime. The vizier indeed inclined towards Muhammad, but the latter prudently chose to await al-Muktafi's death before accepting. Indeed, the Caliph recovered, and was informed that people were discussing both Ibn al-Mu'tazz and Ibn al-Mu'tamid as his possible successors. This worried al-Muktafi, who in the presence of the qāḍīs as witnesses officially nominated Ja'far as his heir, before dying. The two stories highlight different aspects of al-Muqtadir's accession: on the one hand, a cabal of officials choosing a weak and pliable ruler, "a sinister development" that inaugurated one "of the most disastrous reigns in the whole of Abbasid history a quarter of a century in which all of the work of predecessors would be undone", while on the other hand, the issue of dynastic succession, and especially the loyalty of al-Mu'tadid's ghilmān to his family, evidently also played an important role.