The role of mycotoxins—e.g., aflatoxins, ochratoxins, trichothecenes, zearalenone, fumonisins, tremorgenic toxins, and ergot alkaloids—has been recognized in the etiology of a number of diseases. In many African countries, the public health impact of chronic (indoor) and/or repeated (dietary) mycotoxin exposure is largely ignored hitherto, with impact on human health, food security, and export of African agricultural food products. Notwithstanding, African scientific research reached milestones that, when linked to findings gained by the international scientific community, make the design and implementation of science-driven governance schemes feasible. Starting from Nigeria as leading African Country, this article (i) overviews available data on mycotoxins exposure in Africa; (ii) discusses new food safety issues, such as the environment–feed–food chain and toxic exposures of food producing animals in risk assessment and management; (iii) identifies milestones for mycotoxins risk management already reached in West Africa; and (iv) points out preliminary operationalization aspects for shielding communities from direct (on health) and indirect (on trade, economies, and livelihoods) effects of mycotoxins. An African science-driven engaging of scientific knowledge by development actors is expected therefore. In particular, One health/One prevention is suggested, as it proved to be a strategic and sustainable development framework.