According to the philologist-historian Paul Kraus (1904-1944), Jabir cleverly mixed in his alchemical writings unambiguous references to the Ismaili or Qarmati movement. Kraus wrote, 'Let us first notice that most of the names we find in this list have undeniable affinities with the doctrine of Shi'i Gnosis, especially with the Ismaili system'. Henry Corbin believes that Jabir ibn Hayyan was an Ismaili. Jabir was a natural Philosopher who lived mostly in the 8th century; he was born in Tus, Khorasan, in Persia, well known as Iran then ruled by the Umayyad Caliphate. Jabir in the classical sources has been variously attributed as al-Azdi al-Barigi or al-Kufi or al-Tusi or al-Sufi. There is a difference of opinion as to whether he was a Persian from Khorasan who later went to Kufa or whether he was, as some have suggested, of Syrian origin and later lived in Persia and Iraq. His ethnic background is not clear, but most sources reference him as a Persian. In some sources, he is reported to have been the son of Hayyan al-Azdi, a pharmacist of the Arabian Azd tribe who emigrated from Yemen to Kufa (in present-day Iraq) during the Umayyad Caliphate. while Henry Corbin believes Geber seems to have been a non-Arab client of the 'Azd tribe. Hayyan had supported the Abbasid revolt against the Umayyads, and was sent by them to the province of Khorasan to gather support for their cause. He was eventually caught by the Umayyads and executed. His family fled to Yemen, where Jabir grew up and studied the Quran, mathematics and other subjects. Jabir's father's profession may have contributed greatly to his interest in alchemy.

The identity of the author of works attributed to Jabir has long been discussed. According to a famous controversy, pseudo-Geber has been considered as the unknown author of several books in Alchemy. This was first independently suggested, on textual and other grounds, by the 19th-century historians Hermann Kopp and Marcellin Berthelot. Jabir, by reputation the greatest Chemist of Islam, has long been familiar to western readers under the name of Geber, which is the medieval rendering of the Arabic Jabir, the Geber of the Middle Ages. The works in Latin corpus were considered to be translations until the studies of Kopp, Hoefer, Berthelot, and Lippman. Although they reflect earlier Arabic alchemy they are not direct translations of "Jabir" but are the work of a 13th-century Latin Alchemist. Eric Holmyard says in his book Makers of Chemistry Clarendon press.(1931).

The question of Pseudo-Gebers identity is still in dispute (1962). It is said that Geber, the Latinized form of "Jabir," was adopted presumably because of the great reputation of a supposed 8th-century Alchemist by the name of Jabir ibn Hayyan. About this historical figure, however, there was considerable uncertainty a century ago, and the uncertainty continues today. This is sometimes called the "Geber-Jābir problem". It is possible that facts mentioned in the Latin works, ascribed to Geber and dating from the twelfth century and later, may be placed to Jabir's credit.

In 988 Ibn al-Nadim compiled the Kitab al-Fihrist which mentions Jabir as a spiritual follower and as a companion to Jafar as-Sadiq, the sixth Shia Imam. In another reference al-Nadim reports that a group of Philosophers claimed Jabir was one of their own members. Another group, reported by al-Nadim, says only The Large Book of Mercy is genuine and that the rest are pseudographical. Their assertions are rejected by al-Nadim. Joining al-Nadim in asserting a real Jabir; Ibn-Wahshiyya ("Jaber ibn Hayyn al-Sufi ...book on poison is a great work...") Rejecting a real Jabir; (the Philosopher c. 970) Abu Sulayman al-Mantiqi claims the real author is one al-Hasan ibn al-Nakad al-Mawili. The 14th century critic of Arabic literature, Jamal al-Din ibn Nubata al-Misri declares all the writings attributed to Jabir doubtful.

In 2005, the Historian Ahmad Y. Al-Hassan pointed out that earlier Arabic texts prior to the 13th century, including the works of Jabir and Al-Razi, already contained detailed descriptions of substances such as nitric acid, aqua regia, vitriol, and various nitrates. In 2009, Al-Hassan criticized Berthelot's original hypothesis and, on textual grounds, argued that the Pseudo-Geber Corpus was originally written in Arabic. Al-Hassan criticized Berthelot's lack of familiarity with the complete Arabic corpus and pointed to various Arabic Jabirian manuscripts which already contain much of the theories and practices that Berthelot previously attributed to the Latin corpus. Regardless of the identity of pseudo-Geber, the contents of the Pseudo-Geber Corpus are mostly derived from earlier Arabic alchemy, including the work of Jabir as well as other Arabic authors such as Al-Razi.

As early as the 10th century, the identity and exact corpus of works of Jabir was in dispute in Islamic circles. His name was Latinized as "Geber" in the Christian West and in 13th-century Europe an anonymous Writer, usually referred to as Pseudo-Geber, produced alchemical and metallurgical writings under the pen-name Geber.

Whether there was a real Jabir in the 8th century or not, his name would become the most famous in alchemy. He paved the way for most of the later alchemists, including al-Kindi, al-Razi, al-Tughrai and al-Iraqi, who lived in the 9th–13th centuries. His books strongly influenced the medieval European alchemists and justified their search for the philosopher's stone. In the Middle Ages, Jabir's treatises on alchemy were translated into Latin and became standard texts for European alchemists. These include the Kitab al-Kimya (titled Book of the Composition of Alchemy in Europe), translated by Robert of Chester (1144); and the Kitab al-Sab'een (Book of Seventy) by Gerard of Cremona (before 1187). Marcelin Berthelot translated some of his books under the fanciful titles Book of the Kingdom, Book of the Balances, and Book of Eastern Mercury. Several technical Arabic terms introduced by Jabir, such as alkali, have found their way into various European languages and have become part of scientific vocabulary.

By Jabirs' time Aristotelian physics had become Neoplatonic. Each Aristotelian element was composed of these qualities: fire was both hot and dry, earth, cold and dry, water cold and moist, and air, hot and moist. This came from the elementary qualities which are theoretical in nature plus substance. In metals two of these qualities were interior and two were exterior. For Example, lead was cold and dry and gold was hot and moist. Thus, Jabir theorized, by rearranging the qualities of one metal, a different metal would result. Like Zosimos, Jabir believed this would require a catalyst, an al-iksir, the elusive elixir that would make this transformation possible — which in European alchemy became known as the philosopher's stone.