The contribution of Muslims in the spread of education during their rule in South Asia is tremendous. Even during the political decline of the Mughal Empire, the educational system thrived and survived. However, as colonial rule took root along with the British educational system, the Muslim community struggled to maintain their traditional educational institutions. However, several of these institutions inducted new trends and ideas in their syllabi which also became a target of controversy and debate. This paper presents a study of such encounters and controversies.