This article examines the structural tension between conflict management and economic integration within IGAD and its implications for the political economy of the Horn of Africa in IGAD with comparative reference to the EAC, SADC, and ECOWAS. It asks how security-crowded regional integration structures political order during the contemporary era of regional security crises and integration planning, combining regional integration theory, the security-development nexus, and African regionalism with a research design centred on institutional analysis of IGAD texts and budgets, comparison with other African regional organisations, trade-flow interpretation, and interviews with regional stakeholders. The central argument is that the issue under study is not best explained as a discrete policy failure or a short-lived crisis. Rather, it is reproduced through linked institutional and political mechanisms that reshape incentives, authority, and access to resources over time (Haas, 1958; Balassa, 1961) (Soderbaum, 2004; Taylor, 2003). Across the paper, the analysis tracks how these mechanisms operate in practice, what variation they generate, and why reform agendas that ignore the underlying political settlement rarely succeed. The article therefore contributes both a conceptual synthesis and a grounded comparative interpretation of the focal case. Its wider implication is that durable reform requires institutional redesign, political bargaining, and accountability strategies capable of reaching the real sites where power is exercised (Bach, 2016; Acharya, 2009) (IGAD, 2024; COMTRADE, 2024).