One major source of conflict was the theoretical expectation that Muslim rulers were to be guided by the ulama, who were expected to ensure that they ruled according to the shari'a. However, the situation was complicated in the subcontinent, where there were populations that did not subscribe to Islam, creating tension between religious principles and political realities.

Another source of conflict arose when religious leaders declined royal gifts, as seen in the case of Shaikh Nizamuddin Auliya's hospice. Such refusals demonstrated the independence of religious figures from political authority and could strain relationships.

Additionally, some religious leaders who questioned the authority of the Vedas and expressed themselves in languages of ordinary people were not in a position to win the support of the ruling elites. This created a divide between popular religious movements and established political powers.