Many observers worry that growing numbers of international institutions with overlapping functions undermine governance effectiveness via duplication, inconsistency and conflict. Such pessimistic assessments may undervalue the mechanisms available to states and other political agents to reduce conflictual overlap and enhance inter-institutional synergy. Drawing on historical data I examine how states can mitigate conflict within Global Governance Complexes (GGCs) by dissolving or merging existing institutions or by re-configuring their mandates. I further explore how “order in complexity” can emerge through bottom-up processes of adaptation in lieu of state-led reform. My analysis supports three theoretical claims: (1) states frequently refashion governance complexes “top-down” in order to reduce conflictual overlap; (2) “top-down” restructuring and “bottom-up” adaptation present alternative mechanisms for ordering relations among component institutions of GGCs; (3) these twin mechanisms ensure that GGCs tend to (re)produce elements of order over time–albeit often temporarily. Rather than evolving towards ever-greater fragmentation and disorder, complex governance systems thus tend to fluctuate between greater or lesser integration and (dis)order.