Acute infection and chronic infection are the two most common fates of pathogenic virus infections. Using the experimental lymphocytic choriomeningitis virus (LCMV) infection model of mice, we show that a temporal difference in cytotoxic T cell-mediated killing of splenic marginal zone CD169+ macrophages is a critical event determining the outcome of the infection. It occurs later in acute infection and thus enables CD169+ marginal zone macrophages to produce a type-I interferon wave that is required for generation of effector CD8+ T cells and virus clearance. However, this comes at a cost for the host in the form of spleen fibrosis. Our findings demonstrate the critical importance of kinetically well coordinated sequential immune events for virus infection control.