Molendijk has extensively published in the history of ideas, in particular on nineteenth- and twentieth-century theology and religious studies. His latest books are The Emergence of the Science of Religion in the Netherlands (Brill, 2005) and Friedrich Max Müller and the Sacred Books of the East (Oxford University Press, 2016). Molendijk is also engaged in research on religion, identity, and the public sphere, and has participated in a research programme on new sacred places and emerging rituals.