Ayatollah Ruhollah Khomeini taught in Qom's seminaries for decades before his political activism, opposing the policies of Iran's ruling Pahlavi monarchy, led to his arrest and 1964 exile. While abroad he developed and taught the doctrine of velayat-e faqih, guardianship of the Islamic jurist, arguing that in the absence of the Twelfth Imam a qualified religious scholar should hold ultimate political authority over the state, a significant departure from the more common Shia view that clergy should stay outside direct governance while the political order awaited the Imam's return.
That doctrine became the constitutional basis of the Islamic Republic of Iran after the 1979 revolution, with Khomeini himself serving as its first Supreme Leader, and it gives Qom's seminaries a political weight that Najaf's "quietist" tradition, associated with figures who hold clerical authority should stay largely separate from day to day governance, deliberately does not claim for itself. The two cities represent genuinely different, actively debated understandings of how religious authority should relate to the state, rather than a single Shia consensus.
The doctrine was never unanimous even within Qom's own seminaries. Grand Ayatollah Hossein-Ali Montazeri, once designated as Khomeini's successor, broke publicly with the government over its human rights record in the late 1980s and spent years afterward under house arrest in Qom for continuing to criticize velayat-e faqih's scope, a reminder that the city's clergy have never spoken with one voice on how far clerical authority over the state should extend.