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Like his father, Muhammad al-Bakir was politically quiescent and refrained from openly putting forward any claim. During his time, there was a rival claimant for the allegiance of the Shiites. This was his half-brother, Zaid, who advocated a more politically active role for the Imam and was prepared to accommodate to a certain extent the view-point of the majority of Muslims by acknowledging the caliphates of Abu Bakr and Umar.
Zaid had asserted a claim to the Imamate on the basis that it belonged to the descendant of Ali and Fatima, who must come forward publicly for his claims for Imamate and Caliphate. He believed that if an Imam wanted to be recognized, he had to claim his right with a sword in hand. Thus, the first Alid of the Hussainid line who rose against the Umayyads was Zaid.

The popularity of Zaid's movement overshadowed Muhammad al-Bakir's efforts to attacking only the friends and followers of Zaid. Nevertheless, he did not hesitate to contest Zaid's claim. However, al-Bakir and Zaid quarrelled over this point, for when the latter asserted that an Imam must rise against the oppressors, the former remarked: 'So you deny that your own father was an Imam, for he never contested the issue.' The disagreement between al-Bakir and Zaid had arisen when the latter incorporated the teachings of a Mutazilite, Wasil bin Ata. In the course of time, al-Bakir succeeded in winning back some of those who had gone over to Zaid. The most important of them were Zurara bin Ayan, his brother Humran, and Hamza bin Muhammad bin Abdullah at-Tayyar etc.

Zaid, by adhering to Wasil bin Ata and his doctrines, gained good support of the Mutazilites, and his acceptance of the legitimacy of the first two caliphs earned him the full sympathy of the traditionist circles. Finally, Zaid's revolt against the Umayyads took place in Safar, 122/December, 740 when he came forward and summoned the people to espouse his cause. Zaid was warned by his brother, Muhammad bin Ali bin Hussain, not to put any reliance on the people of Kufa, but Zaid did not notice his brother's warning and led the Kufans in a vain rebellion. This occurred in the reign of caliph Hisham. Yousuf bin Umar Thaqafi, the governor of the two Iraks, dispatched Abbas al-Murri with an army against Zaid. He was struck by an arrow, and died of his wound. Zaid's son Yahya fled to Khorasan and led an uprising after three years. He too was overcome, and killed in 125/743 and met the same fate as his father. Later on, the Zaidiyya recognized no designation for the Imamate, nor any strict hereditary principle. Thus the movement of Zaid however ended in failure, paved the way for other claimants and offered ready ground for a more effective revolt.

Muhammad al-Bakir was the first to establish the start of legal school of Ahl-al-Bait in view of the prevalent milieu. Kashi records for us an important tradition in his 'Rijal' (p. 289) that, 'Before the Imamate of Muhammad al-Bakir, the Shias did not know what was lawful and what was unlawful, except what they learned from the people; until Abu Jafar (al-Bakir) became the Imam, and he taught them and explained to them the knowledge (of law), and they began to teach other people from whom they were previously learning.' This tradition clearly indicates that until the time of Muhammad al-Bakir, there were hardly any differences in legal practices among the Shiites of Medina, Kufa and elsewhere. This was an earliest move in the formation of the Shiite jurisprudence.