This research examines the relationship between the Catholic Church and the military regimes in Latin America in the latter half of the twentieth century. Although prevailing theories explain church behavior regarding authoritarianism in reference to Protestant competition, I argue that church opposition is best explained by institutional arrangements in two ways. First, whether the church opposes authoritarianism is contingent on the degree of institutional autonomy the church possesses. Secondly, the strength of the opposition depends upon the presence of structural carriers, which are institutions connecting the church to society. The cases of Chile, Argentina, and Uruguay are examined through a historical institutionalist lens to test these hypotheses. Findings from these historical case studies indicate that both institutional autonomy and structural carriers are necessary for opposition. Ultimately, this study sheds light on the question of why religious institutions operate in varying ways in similar political contexts. It is also a contribution to the “path dependent model,” which posits that the history of institutional arrangements serves as a strong influence on contemporary institutional behavior.