This article addresses the South American difficulties in the consolidation of regional security mechanisms, developing an analytical model called the “paradox of autonomy.” This model was developed through the application of inductive and deductive methodological criteria, based on the observation of recent historical reality, in order to attain generalizable lessons from a relevant case for South American international relations. Also using rational analytical approaches that allow their construction within the framework of rational action problems. From the observation on the emergence and performance of the South American Defense Council, it was identified that the allowing conditions for a novel mechanism of regional (collective) autonomy for security, paradoxically offered opportunities for the exercise of national (individual) autonomy. The article concludes that, although the conditions for the paradox of autonomy are difficult to overcome in cases of security regionalism initiatives, there are possibilities to do so. The key would be in less ambitious institutional designs that recognize the inherent difficulties for institutional regional security cooperation in South America.