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Two plant production-based strategies – biofortification and dietary diversification – have been advocated to overcome micronutrient deficiencies, which are major contributors to morbidity and mortality worldwide. The respective benefits and effectiveness of these two strategies are the subject of controversy. Expanding the scope of this debate beyond the sole nutritional outcomes, and using a food system approach, this interdisciplinary review aims to providing a novel and holistic perspective on the ongoing debate. The literature shows that biofortification can be an effective medium-term strategy to tackle nutritional risk in vulnerable populations in some contexts, but that it also may have negative environmental, economic, and social impacts. Dietary diversification, on the other hand, is known to be a sustainable way to overcome micronutrient deficiencies, bringing with it long-term benefits, including nutritional, and beyond, the provision of ecosystem services. Dietary diversification is however challenging to implement, with benefits that are not immediate. Biodiversity as a basis of human diets is critically important to improving both human and environmental health. Diet diversification through increased mobilisation of biodiversity in food systems deserves much more attention and support in policies for food and nutrition in low- and middle-income countries.