From the moment he returned to Tehran on February 1, 1979, Khomeini’s frail appearance prompted speculation about his health, placing the question of succession into focus from the outset of the Islamic Revolution. In the spring of 1980, he suffered a minor heart attack, further heightening the urgency of tackling the issue of succession. Once the regime had gained the upper hand in quelling the MEK-led insurgency, Khomeini ordered an election for the Assembly of Experts, the clerical body constitutionally tasked with selecting a successor for the role of Supreme Leader, in December 1982.

Khamenei was one of the 83 clerics chosen for the original Assembly of Experts, although he did not have a leadership role. Rafsanjani was also elected to the Assembly and, given his stature within the regime, was made one of two deputy chairmen of the Assembly. At the same time, Ayatollah Meshkini, an ally of Khamenei, was designated as the chairman of the Assembly.      

The Islamic Republic’s original 1979 constitution essentially tailored the qualifications for Supreme Leader to describe Ayatollah Khomeini. According to the constitution, the role of velayat-e faqih could only be assumed by a recognized marja-e taghlid, a cleric holding the title of Grand Ayatollah or Imam who was universally recognized within the Shi’a world as a source of emulation. At the time, few clerics could claim Khomeini’s religious and revolutionary qualifications, and his appointment was a fait accompli. According to the constitution, if a suitable replacement did not exist, a council of three to five senior clerics would instead be needed to fill the role of Supreme Leader.

The Assembly of Experts began convening to designate a successor to Khomeini in July 1983. Khomeini provided the Assembly a sealed envelope containing his political testament, the contents of which have never been made public and may not have even been known to Assembly members. He implored the Assembly to choose a successor “for the sake of God and for God alone,” an exhortation to the Assembly members not to let personal ambition or factionalism cloud their judgment. However, such earthly considerations certainly played into the process.

No other individual cleric in Iran could claim Khomeini’s religious and political stature, which made selecting his successor difficult. Most of those who had attained the necessary religious credentials were advanced in age and more traditionalist and orthodox, rejecting core Khomeinist principles. They opposed the doctrine of velayat-e faqih and felt clerics should stay out of the political realm. Khomeini’s hatred for the orthodox clergy rivaled his hatred for the U.S., as he felt they were reactionaries whose advocacy of quietism made them tools of corrupt leaders. Khomeini insisted that only adopting his revolutionary ideology could lead to the liberation of the oppressed.   

Two schools of thought emerged within the Assembly of Experts over who should succeed Khomeini. The first backed Ayatollah Hossein-Ali Montazeri, the next senior-most cleric behind Khomeini who backed velayat-e faqih and Khomeini’s revolutionary worldview. Montazeri was presumed to be Khomeini’s choice to succeed him, as his son and chief-of-staff, Ahmed Khomeini, had described him as the most suitable successor. Montazeri lacked the charisma and religious qualifications of Khomeini. However, he had been a loyal student of the Imam who ingratiated himself into his inner circle, sharing his radicalism and commitment to export the revolution. Khomeini’s affection for Montazeri was so great that he frequently called him “the fruit of my life.”

Montazeri had been part of the revolutionary struggle against the Shah, enduring periods of imprisonment and exile. Upon establishing the Islamic Republic, he was made Tehran's first Friday prayer leader and served as the President of the Assembly of Experts that produced Iran’s 1979 constitution. After these prominent postings, however, he faded from the political scene and was quickly overshadowed by other clerics such as Khamenei, Beheshti, Rafsanjani, and Mousavi. It was believed that Montazeri, a soft-spoken religious leader, had little interest in power politics. In many ways, this lack of personal ambition made him an ideal candidate for the Supreme Leader post, as his only concern would be with upholding the ideals of the Islamic Revolution.

The second faction in the Assembly of Experts preferred a leadership council to take over the role of the Supreme Leadership after Khomeini’s passing. Those advocating this path felt that there was no worthy successor to Khomeini and that a council would allow representation from multiple factions, helping mend the split between left and right and ensuring that the leadership would need to commit to compromise, which would, in turn, ensure a moderate approach to governance.

According to a 1983 CIA assessment, Rafsanjani and Khamenei were two of the key power brokers jockeying for personal power and influence over the trajectory of the post-Khomeini Islamic Republic. Neither had the religious qualifications to succeed Khomeini directly, so Rafsanjani favored Montazeri’s succession, believing Montazeri could sideline the conservative clerics completely could manipulate Montazeri. With Montazeri likely to be isolated in Qom, Rafsanjani could become the dominant political influence in Tehran. Khamenei, meanwhile, favored a three-to-five-member leadership council, as he felt he would likely have close ties and ideological affinities with several of the likeliest choices to serve on the council, giving him a foothold for influence that he would lack if Montazeri assumed sole power.

After more than two years of deliberation, the Assembly of Experts announced that it had chosen Montazeri as the heir apparent for the Supreme Leadership in November 1985. Montazeri was also named deputy Supreme Leader, although Khomeini did not delegate many additional responsibilities to him, and the role was largely symbolic. Over time, particularly after the end of the Iran-Iraq War, Montazeri fell out of favor with Khomeini, leading to a succession crisis. Unconcerned with his political fortunes, Montazeri became the most prominent voice in Iran, criticizing the government for its lack of military, economic, and political strategy in its conduct of the war. His time in the Shah’s prisons had also imbued him with a genuine sensitivity to the plight of political prisoners detained unjustly and inhumanely, which had increasingly become a feature of the Islamic Republic during Khomeini’s rule. He remained a passionate defender of velayat-e faqih but advocated for a more open system for political criticism and more direct democratic participation. In his view, the Islamic Republic under Khomeini had devolved into a dictatorship, and he expressed this view openly.

Things came to a head after the 1988 purge of Iranian prisoners. Montazeri opposed the spate of executions on moral and strategic grounds, arguing in a series of private letters to Khomeini that it was counter to the principles of Islam to execute one’s captives, particularly when the arbitrary nature of the trials made it likely that innocent prisoners would likely be executed. In his view, the purge would turn international opinion against the Islamic Republic and become Iran’s enduring legacy, harming the nation’s interests. During this period, Montazeri also addressed judicial officials behind the purge campaign, urging them to reconsider. In leaked audio of this meeting that his family members released in 2016, Montazeri warned the judges, “In my view the biggest crime in the history of the Islamic republic, for which history will condemn us, has been committed at your hands. Your names will be written in history as criminals."

Khomeini was unmoved by Montazeri’s opposition, maintaining that anyone who took up arms against the Islamic Republic deserved execution. Subsequently, Montazeri went increasingly public with his criticisms of the purges and the dictatorial evolution of the Islamic Republic itself. In early 1989, in a speech given as part of the national celebration marking the 10th anniversary of the revolution, Montazeri gave his most forceful denunciation of Khomeini’s rule, an unprecedented rebuke from a prominent figure within the regime.

In his speech, Montazeri argued that Iran’s revolutionary obstinacy had left it isolated in the world, that Khomeini’s repression had broken the spirit of unity that existed in the early days of the revolution, and that the rudderless leadership of the war effort had led to defeat and needless deaths among the youth of the nation. He said that those who were committed to the ideals of the revolution should be free to criticize Iran’s leadership without fear of persecution for straying from those ideals so long as their expression was in service of advancing the revolutionary cause. He concluded with his most incendiary attack yet, saying that if Khomeini’s Islamic government required the country to compromise its values and principles, it was preferable not to have an Islamic government.

Montazeri’s attack was a repudiation of the evolution of Khomeini’s worldview. It contained echoes of a previous incident that had occurred in early 1988 regarding the issue of static vs. dynamic fiqh (jurisprudence). In this instance, Khomeini had ruled that the state could punish individuals or companies who were hoarding resources or not paying taxes without a trial, an expansion of executive powers. The conservative-dominated Guardian Council took exception and argued to Khomeini that his decree would open the door for the government to intervene in economic affairs outside the established framework of sharia. Khomeini reaffirmed his ruling, which prompted Ali Khamenei to give a sermon in which he stated his understanding of Khomeini’s ruling was that “the government can require the employer to observe a series of regulations and duties, this does not mean that accepted Islamic decrees are no longer valid...the Imam has said that the government can order the employer to observe certain conditions, but the conditions must be within the framework of accepted Islamic decrees.” Effectively, Khamenei said that the government was bound to act within the established Islamic law.

Khomeini responded with a rare rebuke of Khamenei carried by the state-run media apparatus. In Khomeini’s formulation, which represented the final evolution of his political thought, the imperative of the survival of the Islamic state was paramount, superseding even the rules of Islam. The Supreme Leader could effectively pass any rule or decree that he deemed necessary to ensure the survival of the Islamic Republic. By nature of the divine authority of his Supreme Leadership, that rule would inherently become canonical under Islamic law. In issuing this corrective, Khomeini declared that the Supreme Leader’s power was absolute and that the Supreme Leader was infallible.

Despite the ugliness of the row, Khamenei accepted Khomeini’s declaration of absolute power. Khomeini, loath to create a political crisis, indicated publicly that Khamenei retained his full confidence. The incident was instructive for Khamenei, who, after taking on the mantle of Supreme Leadership, has governed in an absolutist manner, placing his conception of the exigencies of the survival of the Islamic Republic above all other considerations, including established Islamic precedent. Thus, as Supreme Leader, Khamenei had resorted to repression without compunction and fought to usurp power from each president who had served under him when their agendas conflicted with his vision. Khamenei’s adherence to Khomeini’s vision also helps explain the extralegal steps Khamenei has taken in the twilight of his own Supreme Leadership to trample over the more democratic elements of the hybrid system he inherited and marginalize pragmatic voices to ensure that the Islamic Republic remains in the hands of its most strident, hardline partisans with leadership authority fully vested in the Supreme Leader and the IRGC.

Montazeri’s broadsides against Khomeini and the increasingly anti-democratic system he had propagated poisoned whatever goodwill the Imam may have retained for his former favorite pupil. In early March, the letters Montazeri had penned to Khomeini criticizing the 1988 prison massacres were somehow obtained by exiled opposition leader and former first president of the Islamic Republic, Abolhassan Banisadr, in Paris and were broadcast by the international press. This leak alerted the world and the Iranian public to the extent of the Islamic Republic’s criminality in carrying out the purges, which it had sought to keep under wraps. An enraged Khomeini summoned the Assembly of Experts to convene after the publication of Montazeri’s letters and reexamine the issue of leadership after his death. Ahead of the meeting, Khomeini summoned several of the senior-most members of his inner circle, including the head of the Assembly, Ayatollah Meshkini, Rafsanjani, and Khamenei, to meet with him. The meeting attendees counseled Khomeini that it would harm the interests of the Islamic Republic to publicly remove Montazeri as designated successor since no other qualified individuals were waiting in the wings to replace him. At this point, Khomeini reportedly replied, “but you have Mr. Khamenei who is eligible.”

It is unclear whether Khomeini endorsed Khamenei in this manner or if Khomeini’s endorsement was manufactured after the fact to justify Khamenei’s succession despite his constitutional lack of suitability for the role. Regardless, the meeting between Khomeini and his inner circle led to Khamenei’s selection as his designated successor.

Khomeini divulged in the meeting that he had written a scathing letter denouncing Montazeri that he intended to publicize. However, at the urging of the attendees, he decided to send the letter privately to Montazeri. The letter, which was eventually released, can be read in full in Baqer Moin’s biography of Khomeini. In it, Khomeini tells Montazeri, “Since it has become clear that after me you are going to hand over this country, our dear Islamic revolution, and the Muslim people of Iran to the liberals, and through that channel to the hypocrites [the Mojahedin-e Khalq], you are no longer eligible to succeed me as the legitimate leader of the state. … I swear to God from the start I was against choosing you as my successor, but at the time I did not realize you were so gullible. … If you continue your deeds, I will definitely be obliged to do something about you. And you know me, I never neglect my obligation.”

Montazeri accepted his forced resignation, and on March 28, 1989, Khomeini made a public statement informing the Islamic Republic that he had opposed Montazeri’s succession and accepted his resignation. This was the first the public learned of the discord behind the scenes among the upper echelons. Montazeri jarringly went from revered Grand Ayatollah and hope of the Islamic Republic to persona non grata overnight.

With Khomeini’s health fading, the issue of succession became a pressing crisis, particularly due to the lack of a suitable candidate. Those who had obtained the level of marja-e taghlid, either opposed the doctrine of velayat-e faqih or lacked the political and managerial acumen needed for the role. On April 24, 1989, Khomeini invoked his special powers as Supreme Leader to form a 25-member Assembly for Revising the Constitution, including Khamenei, Rafsanjani, and Mousavi. The Assembly set about amending the constitution for the first and only time in the Islamic Republic’s history to smooth the succession process and clarify the government’s power structure to ease the bottlenecks that had paralyzed policymaking during the 1980s.

On Khomeini’s direct instruction, the Assembly did away with the provisions in Article 109 of the 1979 Constitution, which required the Supreme Leader to be a marja-e taghlid and allowed for a committee to assume the role without a qualified individual successor. This represented a major dilution of the velayat-e faqih position, as Khomeini theorized in his seminal work, Islamic Government. The Supreme Leader’s authority was supposed to be derived from his established recognition as a leading religious authority and source of emulation in the Shi’a world, which made him a vessel capable of interpreting and carrying out God’s will. In a letter responding to an inquiry of his views on the qualifications for a Supreme Leader from Ayatollah Meshkini, the head of the Assembly of Experts, dated April 29, 1989, Khomeini claimed that he never felt the Supreme Leader needed to be a marja-e taghlid. This was a self-serving revision of his life’s work. Khomeini wrote, “From the very beginning, I believed and insisted that there is no need for the requirements of marjaʿiyyat. A pious mujtahid, who is approved by the esteemed Assembly of Experts shall suffice. … In this case, he is the elected valī and his decree is binding.”

Accordingly, the constitutional assembly amended Article 109 and required the Supreme Leader to possess sufficient scholarship to exercise Islamic jurisprudence and strong political and managerial acumen. Thus, the Supreme Leader would now be viewed more as a political than religious position. He would be more reliant on the state going forward to derive authority, as opposed to Islam, weakening the argument that Iran’s reigning theocrat decreed by divine fiat. Khamenei backed these reforms, arguing that Khomeini’s success in leading the Islamic Revolution and shepherding the Islamic Republic through its first decade was the result of his political wisdom and courage coupled with his jurisprudential expertise, rather than just his authority as a marja. Rafsanjani concurred, noting that by the time an individual reached the level of Grand Ayatollah, he would likely be too old and enfeebled to manage state affairs effectively. The Assembly also removed a provision requiring the Supreme Leader to be supported by the majority of the populace, claiming that because the Assembly of Experts was popularly elected, its selection inherently enjoyed popular support. In effect, claims going forward that the Supreme Leader ruled by divine will or popular acclaim were weakened by the dilution of the qualifications for the position.

While the constitutional amendments weakened the vali-e faqih’s religious and popular legitimacy, they simultaneously enhanced his political powers, setting the stage for the role to evolve in a more authoritarian, dictatorial direction. The most consequential new power granted to the Supreme Leader was the authority to set and supervise the general policies of the Islamic Republic in accordance with his vision for the nation's best interests. The republican elements would carry out the day-to-day administrative functions and have a policy-making role, but effectively, they would work to carry out the Supreme Leader’s overarching agenda. The Supreme Leader was also placed in charge of commanding the armed forces, declaring war and peace, and controlling leadership appointments within the military and security forces, judiciary, and state media apparatuses. 

The new constitution also sought to streamline the Islamic Republic’s republican governance. Rafsanjani, the presumptive favored nominee in the presidential elections later that year, sought to use his influence in the constitutional assembly to weaken the faqih and strengthen the presidency. He argued that the Supreme Leader should not have a major policy role, as that would render the president and majles superfluous, and that the Supreme Leader should only serve a 10-year term, but was overruled on both counts. His efforts to strengthen the presidency, however, bore fruit. Khamenei, who had been hamstrung by the weakness of the president’s office throughout his term, backed Rafsanjani’s reforms. At the same time, Mousavi, who had done the bulk of the hamstringing, led the opposition. Ultimately, Khamenei and Rafsanjani won out, and the president’s powers were expanded while the position of prime minister was eliminated. The president took over the prime minister’s role and was now the primary seat of power for day-to-day policymaking. The president was additionally placed in charge of cabinet formation, given increased economic and foreign policy powers, and was in charge of the planning and budget organization and the Supreme National Security Council (SNSC), which coordinates defense, intelligence, and foreign policy.