Muslim control over the Indian subcontinent, especially in areas south of modern Pakistan, was always somewhat precarious. Whatever Muslim dynasty happened to be in power at any given time was guaranteed to be part of a religious minority ruling over a vast number of Hindu subjects. The Mughal Empire, which ruled northern India, modern Pakistan, and modern Bangladesh for most of its lifespan and expanded deep into southern India in the late 17th century, had to manage this problem throughout its history, which led to some interesting developments like Emperor Akbar’s (d. 1605) Din-i Ilahi movement, which emphasized religious tolerance and combined elements of Islam and Hinduism (and other faiths) into an imperial religious syncretism that was intended to win broad acceptance among all of his subjects. Of course the Mughals also ruled sizable Muslim populations in the Sindh region and in Bengal, so they weren’t entirely without a natural base of support. But, again, that base constituted a minority of their subjects and they had to take that into account.
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