Beginning in 1609, as a result of the Capitulations concluded between France and the Ottoman Empire, the French Jesuits launched their missionary work in Istanbul. Protected by the French ambassador, the French Jesuits defined themselves as both French subjects and Catholic missionaries, thus experiencing in a new and complicated geopolitical context the tensions that were at the core of their order’s identity in France, as elsewhere in Europe. The intricate story of the French Jesuit mission to the Ottoman Empire is here considered through two snapshots. One focuses on the foundational period of the mission in Istanbul, roughly from 1609 to 1615. A second one deals with the temporary suspension of the Jesuits’ mission in Istanbul in 1628. These two episodes illustrate multilayered and lasting tensions between the French and the Venetians, between the hierarchy of the Greek Orthodox Church and Western missionaries, and between missionaries belonging to different Catholic orders, between the Roman church’s centralism and state-funded religious initiatives. Based on missionary and diplomatic correspondence, the article is an attempt to reconstitute the way in which multiple allegiances provided expedient tools for individual Jesuit missionaries to navigate conflicts and to assert their own understanding of their missionary vocation.