In the ongoing debate regarding the construction of the modern concept of “Hinduism”, recent research has considered the ways in which the pre-colonial encounter with Islam may have served as a catalyst in the crystallisation of an increasingly self-aware “Hindu” identity. Andrew Nicholson (Unifying Hinduism, 2010), in particular, has examined the genre of Sanskrit doxography to affirm that such a process of crystallisation was indeed taking place, as the transformations in this genre over time indicate a nascent Hindu identity emerging in the face of the “Muslim threat”. This article reevaluates Nicholson's account with reference to the writings of one Sanskrit intellectual operating at the height of Muslim power in South Asia: the figure of Madhusūdana Sarasvatī (fl. sixteenth-early seventeenth centuries). Madhusūdana's short doxography, the Prasthānabheda, often features in arguments for the pre-colonial roots of the concept of “Hinduism”; Madhusūdana's other doxographical writings, however, are typically neglected. Based upon an analysis of Madhusūdana's Siddhāntabindu and Vedāntakalpalatikā, this article suggests that a more nuanced consideration of the different audiences and authorial intentions that different doxographers had in mind can offer a modified picture of how early modern Sanskrit intellectuals were responding to the Muslim presence in the subcontinent.