Khamenei understood that true longevity in the position would require more than trying to cloak himself in his predecessor’s aura. Khamenei would eventually need to be seen as a legitimate religious authority and source of emulation in his own right, capable of issuing decrees that would carry weight with the Shi’a faithful. When he assumed the Supreme Leadership, Khamenei was politically precarious. However, the powers afforded him by dint of his position helped him quickly establish patronage links that gave him a base and networks of support. Still, the 1989 constitutional amendments had effectively created a fault line between religious and political authority in Iran by diluting the religious qualifications of the Supreme Leader. Khamenei’s lack of religious credentials represented a potential vulnerability, especially if the clerical hierarchy sought to challenge his authority.

The Assembly of Experts recognized the need to buttress Khamenei’s religious credentials to legitimize his rule. It pronounced him an Ayatollah (Sign of God) virtually overnight, elevating him from the mid-ranking title of hojatoleslam (Authority of Islam). Khamenei sought to dress the part, eschewing his outward appearance as an intellectual, pipe-smoking cleric who wore a stylish cloak in favor of the more austere garb worn by traditional clerics.  

Despite the vote of confidence in his leadership by the political echelon, the recognized marjas in Iran were slow to signal their approval of Khamenei as the highest authority in the land, given his junior religious credentials. A week passed after his election, and none had congratulated Khamenei, so Rafsanjani began applying pressure. Finally, a 95-year-old marja, Grand Ayatollah Mohammad Ali Araki, sent Khamenei a series of complimentary letters, which Khamenei and his allies pounced on as a sign of his legitimacy. It is believed that Araki, who was theologically opposed to velayat-e faqih during his career, was not fully in control of his mental faculties then and that his son likely wrote the letters out of political expedience.

Recognizing that he lacked the respect of the senior clergy, Khamenei moved slowly at first to build up his religious authority and then to exert control over the clerical bureaucracy. One of the most potent tools he had at his disposal was his control over the state’s media apparatus, and he used this to build up a cult of personality around himself. State TV broadcast Khamenei’s image more vociferously than it had Ayatollah Khomeini’s to cultivate an image of holiness, and the Islamic Republic of Iran Broadcasting (IRIB) also distributed hundreds of thousands of posters, CDs, and other forms of media to tout him as an earthly deputy of the Hidden Imam and make him a ubiquitous presence in Iran. 

Khamenei treaded cautiously during the first three years of his Supreme Leadership, not pressing to be regarded or followed as a religious authority in the early going. Over time, he would become increasingly assertive in that regard, but at the beginning, the institution of the Supreme Leadership was decoupled from the realm of dispensing fiqh (Islamic jurisprudence), with the senior grand ayatollahs and major seminaries under their control given latitude to operate largely independently and issue rulings which would be binding on their followers with minimal interference from the state. Khamenei was armed with his predecessor’s decree that the interests of the Islamic Republic superseded established Islamic Law, which would, in theory, enable the Supreme Leader to overrule the fatwas of more senior clerics, but he refrained from doing so at first to avoid a clerical mutiny.

As he became more politically secure in the velayat-e faqih role, Khamenei began to test the waters of expanding his religious authority. In March 1992, he issued his first fatwa, ruling that it was permissible to transplant an organ from a living individual who was functionally braindead if the transplant would save a life. Fearing political repercussions, the senior grand ayatollahs opted not to challenge Khamenei’s ruling, paving the way for him to begin occasionally weighing in on matters of fiqh.

Several grand ayatollahs died quickly during the early 1990s, moving Khamenei up the clerical pecking order with each passing. His deputies, most notably Judiciary head Ayatollah Mohammad Yazdi, a staunch Khamenei loyalist, urged the followers of these ayatollahs to transfer their loyalty and charitable contributions to Khamenei after each successive death, with hopes of eventually positioning him as the sole marja-e taghlid in the country. In Yazdi’s view, because an Islamic state had now been established, it was no longer appropriate to have multiple sources of emulation. Having marjas outside of the governmental apparatus risked the issuance of religious decrees that would flout government policy or otherwise encroach on political affairs. For Khamenei to truly be the Supreme Leader of the Islamic Republic, it was therefore vital to recognize him as the sole marja and fuse religious and political authority in the singular personage of the velayat-e faqih. This would strengthen the Khomeinist foundations of the Islamic Republic, augment Khamenei’s power domestically, and legitimize Qom as the epicenter of Shi’ism. The Shi’a clerical hierocracy, both within and outside of Iran, opposed Khamenei’s line-jumping. However, Yazdi’s efforts to coronate him failed to gain traction. 

In November 1994, Ayatollah Mohammad-Ali Araki, the prevailing senior-most marja-e taghlid in Iran, passed away. Khamenei’s state-controlled media organs orchestrated a propaganda campaign calling for Khamenei to be recognized as his successor despite his lack of qualifications. Khamenei’s opponents derided his nomination as akin to an attempted coup and an unprecedented encroachment of politics into the religious sphere. Still, the clergy could not rebuff Khamenei too harshly. As a compromise, the Society of Qom Seminary Teachers put forward seven acceptable candidates to be followed as a marja-e taghlid, including Khamenei. This marked an elevation for Khamenei to the rank of grand ayatollah but was also a setback as he had set his sights on becoming the sole marja-e taghlid in Iran. To save face, Khamenei announced that his duties as Supreme Leader were too taxing to seek to become a marja within Iran, but he unilaterally insisted he was to be recognized as a marja outside of the country.  

Stymied in his efforts to amass religious authority on the merits of his credentials, Khamenei changed tacks and applied his penchant for micromanagement to remaking the Iranian clerical bureaucracy so that he became indispensable as its head. Khamenei benefited because the senior-most grand ayatollahs in the country, while opposed to velayat-e faqih, were largely depoliticized. Khamenei worked to increase their reliance on the state for funds and utilized intimidation to ensure they would not speak out too forcefully against his Supreme Leadership. As he grew comfortable in the position, Khamenei sought to streamline the country’s sprawling and disjointed clerical apparatus under the aegis of the Office of the Supreme Leader. The deaths of several successive Grand Ayatollahs who had been respected and prominent advocates of maintaining clerical independence from the state cleared the resistance to Khamenei exerting full control over the clergy.

As early as 1991, Khamenei called for creating a body within the OSL that would oversee the clergy, ensuring its unity and alignment with Islamic Revolutionary theology and values. In an address marking his first visit to Qom as Supreme Leader, he declared his intention to instrumentalize the clergy on behalf of the regime, saying, “Seminaries and religious men cannot be indifferent toward the government and political affairs...This [government] belongs to you, to the clergy, religion; you have no choice. This is an Islamic republic. If you keep a distance, the republic becomes non-Islamic.” Khamenei noted that the clergy faced economic uncertainty and pledged to invest his offices' resources toward providing health insurance and housing, increasing the clergy’s dependence on Khamenei and the state.

In 1995, Khamenei’s vision came to fruition as he established the Supreme Council of Religious Seminaries of Qom. The Supreme Council is responsible for the day-to-day administration of Iran’s seminaries, including control over their finances. Its members are recommended by the nominally independent Society of Qom Seminary Teachers, but all must be approved by Khamenei and the marja of Qom, ensuring there is no deviance from the Supreme Leader’s worldview and commitment to velayat-e faqih. The creation of the Supreme Council paved the way for Khamenei and the OSL to assert dominance over the religious sphere in the Islamic Republic, wresting power away from the major seminaries and recognizing grand ayatollahs.

The Supreme Council created a standardized curriculum adopted by all the Shi’a seminaries under its control, as well as a network of research institutes and libraries affiliated with seminaries that are also under the Supreme Council’s control, ensuring that all intellectual thought coming out of Iran’s seminaries was in line with Khomeinist ideology. According to Khamenei biographer Mehdi Khalaji, himself a former Qom seminarian who followed Ayatollah Montazeri, because of Khamenei’s efforts to centralize control of the clergy, “The role of traditional centers of religious authority – which operated as a religious and political check on the newly formed hierocracy – correspondingly went into steep decline, and a younger generation of clerics reared in Khomeini’s republic came to occupy positions of great religious and political influence.”

Khalaji further elucidates how Khamenei’s reorganization of the clerical bureaucracy increasingly eroded the independence of the country’s marjas by creating a “modern, digitized system that exerts control over clerics’ private lives, public activities, and political orientation.” Marjas formerly had independent offices from which they would make payments to clerics under their guidance, but under Khamenei, all payments became computerized and centralized and required the knowledge and approval of Khamenei’s representatives. Furthermore, Khamenei has used the prodigious assets under his control to assert his financial and religious supremacy over the established marjas, paying clerics much higher salaries than the marjas were able to out of state and OSL coffers. When he declared himself a marja outside Iran’s borders, he was able to collect alms and access resources from the endowments of rich Shi’a communities in Kuwait and the Gulf, which he used to further pad the OSL’s discretionary budget.

Accordingly, the marjas’ independence has been eroded as Khamenei has become the main financier of Iranian clerics. The Islamic Republic of Iran’s revolutionary regime has usurped the marjas’ religious authority to become the dominant authority over the clergy, leading most marjas to align with the government and the notion of velayat-e faqih. This state of affairs has transformed the clergy into a patronage system with Khamenei at the head, fueling corruption. According to Khalaji, “The government underwrites a hefty budget for religious institutions, making today’s Iranian clerical establishment the wealthiest of any period in history. Well-connected clerics and marjas within the Islamic Republic are involved in lucrative business deals, receive exclusive governmental benefits, and can borrow large amounts of money from banks without sufficient guarantees for repayment. Many charities owned by marjas in Iran and high-ranking clerics engage in business through corrupt dealings with the government.”

To further ensure the hegemony of Khomeinist principles in Iran’s religious life, in 1993, Khamenei created the Friday Prayer Policymaking Council, bureaucratizing his control over the selection and oversight of the Friday prayer leaders dispatched to every province in Iran. The council produces weekly bulletins and disseminates talking points to hundreds of preachers around the country, giving Khamenei a powerful mechanism to amplify his worldview and disseminate his views on the pressing religious, social, and political issues of the day. In effect, the council and the army of Friday prayer leaders function like Khamenei’s personal political party, enabling him to organize and conduct outreach to Iranian citizens using the tens of thousands of mosques in the country. Because the Friday prayer leaders are integrated within their respective communities, they serve as an additional set of eyes and ears monitoring activities within the mosques, which serve as the main centers for communal life throughout Iran. Khamenei has focused on appointing younger clerics in their mid-30s to 40s to Friday prayer leader positions, incentivizing younger seminary students to toe the regime’s line and demonstrate fealty to Khamenei and the Islamic Revolution in hopes of receiving one of these plum appointments. This has ensured that the generation of clerics that came of age after the revolution replicated Khomeinist ideology.

Beyond centralizing his control over the clerical establishment and doling out financial incentives, Khamenei has also used repression and intimidation to keep the clergy in line. In 1987, Ayatollah Khomeini created the Special Court of Clergy, a parallel justice system for the clergy that operates outside Iran’s regular judiciary under the complete control of the Supreme Leader. Khomeini created the court as a means of sanctioning dissident clerics, but Khamenei has expanded the court’s purview from Tehran to cities around the country and commissioned the creation of a parallel prison system tied to the clerical court. Under Khamenei, the court has acted with more flagrant disregard for established legal norms and procedures than the secular judiciary, meting out humiliating punishment, imprisonment, and even executions to hundreds of clerics for essentially political offenses at Khamenei’s whim. In addition to the special clerical court, Khamenei has used the intelligence ministry to monitor Iranian clerics' public and private lives. These intimidation and repression tactics deter clerics from deviating from the regime’s ideology or challenging Khamenei’s authority and legitimacy.

While he could not command the respect of his peers to become a marja in his own right, Khamenei used his managerial acumen and penchant for repression to construct new layers of bureaucracy, which ensured the fealty of the clergy to his rule. As a theocratic regime, the Islamic Republic of Iran relies on the clerical bureaucracy and its foot soldiers to promulgate its ideology at home and abroad and serve as the wellspring for the velayat-e faqih’s legitimacy. Whereas the clergy was formerly renowned for its diversity of thought and independence from the state, Khamenei used repression and control of the purse strings to ensure the near-unanimous support of the clergy for the regime’s ideology and his rule as Supreme Leader. The clergy has thus been susceptible to corruption and effectively coopted as a tool for population control. Paradoxically, however, the erosion of the clergy’s independence has undermined the institution’s legitimacy over time and thus weakened its ability to promote the regime and Khamenei’s political authority. As such, the clergy has ceded power over time to the IRGC, portending Iran’s evolution into a military dictatorship with a clerical veneer.