After independence, the Indian government tended to project JMI primarily as an experimental institution à la Gandhi, focused on basic education and social reform. Although religion played a central part in JMI's ethos, the government was more likely to compare JMI to Visva Bharati, Tagore's experimental school in rural Bengal, than to AMU. AMU, by contrast, appeared to be the Muslim university par excellence. For many Muslims, it was a source of pride and a symbol of Indian Muslim culture. The institution epitomised Sayyid Ahmad Khan's efforts to uplift the community and preserve the legacy of the glorious Mughal past. However, due to the widespread support of teachers and students for the Muslim League in the 1940s, the university also came to be seen, in certain quarters, as a symbol of Muslim separatism. Long after the riots had ceased, it remained a lieu de mémoire of partition, crystallising resentment against Muslims’ supposedly communal and disloyal attitude.

Despite this prejudice, Zakir Husain strongly believed that AMU could contribute, more than JMI, to the development of an ‘integrated nationhood’. It was precisely because of its legacy as a centre of Muslim politics and educational reform that the university could, he believed, channel the efforts to ‘revive hope and faith’ among the ‘despondent Muslim masses’ and help them feel part of India's ‘secular democratic state’.

A few Congress leaders, particularly Nehru and Azad, shared a similar vision of the university's mission in post-independence India. In 1951, AMU became, along with Banaras Hindu University (BHU), one of the three central universities under the control of the central government. For Nehru, it was essential to ensure that, despite partition, Indian Muslims would feel part of the Indian nation in order to build a secular stat