Studies have found links between organizational structure and performance of public organizations. Considering the wide variation in uptake of malaria interventions and outcomes across Nigeria, this exploratory study examined how differences in administrative location (a dimension of organizational structure), the effectiveness of administrative processes (earmarking and financial control, and communication), leadership (use of data in decision making, state ownership, political will, and resourcefulness), and external influences (donor influence) might explain variations in performance of state malaria programs in Nigeria. We hypothesized that states with malaria program administrative structures closer to state governors will have greater access to resources, greater political support, and greater administrative flexibility and will therefore perform better. To assess these relationships, we conducted semistructured interviews across three states with different program administrative locations: Akwa-Ibom, Cross River, and Niger. Sixty-five participants were identified through a snowballing approach. Data were analyzed using a thematic framework. State program performance was assessed across three malaria service delivery domains (prevention, diagnosis, and treatment) using indicators from Nigeria Demographic and Health Surveys conducted in 2008 and 2013. Cross River State was best performing based on 2013 prevention data (usage of insecticide-treated bednets), and Niger State ranked highest in diagnosis and treatment and showed the greatest improvement between 2008 and 2013. We found that organizational structure (administrative location) did not appear to be determinative of performance but rather that the effectiveness of administrative processes (earmarking and financial control), strong leadership (assertion of state ownership and resourcefulness of leaders in overcoming bottlenecks), and donor influences differed across the three assessed states and may explain the observed varying outcomes.