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The degree of Salafi radicalization differs across sub-Saharan Africa. Drawing on the theoretical premises of historical institutionalist scholarship and process tracing techniques, the article examines how two states in East Africa have engaged with their Islamic spheres. Kenya and Uganda are selected as they display diverging degrees of radicalization, which are representative of trends elsewhere too. The analysis highlights the effect of national Islamic associations. The Ugandan state previously created a state-led, centralized national Islamic association and thus, early on, established steering capacity in the Islamic sphere. The creation of an organizational gatekeeper in the Islamic sphere helped facilitate subsequent state strategies—including the cooptation of politically assertive Salafis and the containment of jihadi Salafis. Kenya, meanwhile, has failed to create a state-led, centralized national Islamic association. It lacks an interlocutor for the consultation with and the cooptation of religious challengers. By resorting to indiscriminate violence against Salafi clerics and their followers, the Kenyan state has fomented Salafi radicalization. The findings demonstrate that endogenous informal institutional structures effectively counteract religious challengers and enable weak states to contain jihadi terrorist groups.