This study evaluated the relationship between policy formulation, institutional capacity and threat mitigation in Nigeria, where an unprecedented strain from non-traditional threats like violent insurgency, mass abductions, and cybercrime persists despite the National Security Strategy (NSS) blueprint. Grounded in Structural Realism, the research adopted a descriptive survey design to examine how the persistent execution gap affects real-world safety. Primary data were gathered using a structured questionnaire administered to a sample of 200 personnel across state security agencies, the Office of the National Security Adviser, and policy institutions in Abuja, yielding 186 valid responses for analysis. The study used descriptive statistics and the Pearson Product-Moment Correlation Coefficient for data analysis. Findings revealed a strong, positive relationship between effective strategy implementation and threat mitigation (r = 0.684, p < 0.05), demonstrating that structured policy execution directly improves operational security outcomes. Conversely, a significant inverse relationship emerged between institutional capacity bottlenecks and policy execution effectiveness (r = -0.612, p < 0.05). Operational hurdles—particularly inter-agency rivalries, intelligence siloing, funding deficits, and inadequate technological infrastructure—substantially weaken field execution. The study concludes that strategic policy design alone cannot guarantee national stability without addressing internal structural weaknesses. It recommends establishing a centralized joint-intelligence database to eliminate operational siloing and upgrading technological infrastructure alongside field funding to ensure effective security policy enforcement.