Why and how do pathways to regime complexes diverge? Building on insights from the literatures on institutional design and historical institutionalism, we argue that early institutional design choices produce long-term variation in the pace, density, and composition of institutional layers within a regime complex. In a first step, we argue that if an institution becomes focal, this increases the exit costs for member-states to leave. Additional institutional layers become a more likely outcome. In a second step, we argue that depending on the focal organization’s formal or informal design, variegated sovereignty costs inform the additional layering pathways. If a focal organization is formal, sovereignty costs are high for member-states. Consequently, creating additional institutional layers becomes cumbersome, leading to a slow pace of “negotiated layering” and a regime complex characterized by low density and composed of formal and informal institutions. In contrast, low sovereignty costs associated with informal focal organizations enable a rapid process of “breakout layering” resulting in a high density of mostly informal institutions. We develop our argument by examining the evolution of security institutions in Europe and Asia through diplomatic cables, treaty texts, personal memoirs, and policy memos.