A significant literature demonstrates that the presence of historic missionary societies—especially Protestant societies—during the colonial period is significantly and positively associated with increased educational attainment and economic outcomes. However, we know less about the mechanisms underlying the long-run consequences of institutions, as it is commonly very hard to disentangle direct effects from indirect effects. One clear way to do so, however, is to explore the long-term impact of missionary influence in places in which the direct beneficiaries of missionary education are no longer present. The present article considers one such region, the Anatolian region of the Ottoman Empire. Due to the ethnic violence and population movements at the start of the twentieth century, the newfound Turkish nation-state was largely religiously homogenous. This provides us with a unique situation to empirically assess the long-run indirect effects of Christian missionary societies on local human capital. For this purpose, I present an original dataset that provides the locations of Protestant mission stations and schools, Ottoman state-run schools, and Armenian community schools contained within Ottoman Anatolia between 1820 and 1914. Contrary to the common association found in the literature, this study does not find missionary presence to be correlated with modern-day schooling. Rather, I find that regions with a heightened missionary presence and an active Christian educational market perform better on the gender parity index for pretertiary schooling during both the Ottoman and Turkish periods.