The article analyses two delegated governance projects carried out in Ecuador's Amazonian south-east in the twentieth century. In collaboration with the military and public institutions, two Catholic missions, the Salesian and the Franciscan, were central actors in the colonising of an area inhabited by the Shuar. Considering the wider historical and ethnographic regional context and focusing on practices of cultural translation and territorial politics, I discuss the two missions’ divergent governance sensitivities vis-à-vis the Shuar. ‘Governance sensitivities’ refers in this context to the colonial actors’ capability to recognise colonised subjects as culturally distinct. I combine new empirical material from the historical archive of the Franciscans in Zamora with secondary sources in order to analyse how differences between the two missions’ sensitivity and insensitivity to Shuar otherness became especially prevalent in the 1960s and 70s. The divergent ways the Salesians and Franciscans perceived the Shuar colonial subject had consequences for how they engaged in the protection of Shuar land and for how they contributed to facilitating or holding back indigenous political organisation.