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Vaccines against acute infections execute their protective effects almost exclusively via the induction of antibodies. Development of protective vaccines against persisting pathogens lags behind probably because standard immunogens and application regimen do not sufficiently stimulate those circuits in B cell activation that mediate protection. In general, B cell responses against pathogen derived-antigens are generated through complex cellular interactions requiring the coordination of innate and adaptive immune mechanisms. In this review, we summarize recent findings from prototypic infection models to exemplify how generation of protective antibodies against persisting pathogens is imprinted by particular pathogen-derived factors and how distinct CD4(+) T cell populations determine the quality of these antibodies. Clearly, it is the high plasticity of these processes that is instrumental to drive tailored B cell responses that protect the host. In sum, application of novel knowledge on B cell plasticity and complexity can guide the development of rationally designed vaccines that elicit protective antibodies against persisting pathogens.