This chapter delves into the interplay between organizations and institutions, with a particular focus on IGOs’ decision-making processes. The text begins by examining the case of the International Commission against Impunity in Guatemala (CICIG), illustrating the challenges IGOs face in navigating political environments while maintaining legitimacy. The chapter highlights how institutions, though often perceived as rational and technical entities, are deeply embedded in social and political contexts that shape their actions and decisions. The discussion delves further into the concept of institutionalization within intergovernmental organizations (IGOs), emphasizing how the routines and practices that develop over time can stabilize as well as constrain organizational behavior. Utilizing examples such as the World Trade Organization (WTO) and INTERPOL, it highlights the tension between maintaining institutional autonomy and addressing the diverse needs of member states. Moreover, the analysis critically examines the notion of rational decision-making in IGOs. It proposes that although decision-making is often portrayed as a rational process, it is also shaped by social, cultural, and political factors that introduce elements of irrationality. In addition, the chapter discusses the paradoxes and challenges associated with institutional design and reform, particularly in the context of global governance. It highlights how IGOs, despite their technical mandates, are subject to the same limitations of bounded rationality and are influenced by the broader institutional logics in which they operate. The text argues that understanding the relationship between organizations and institutions requires to considers both the formal structures and the informal dynamics that shape decision-making processes.