Obesity is a critical medical condition worldwide that is increasingly involved with nutritional derangements associated with micronutrient deficiencies, including iron, zinc, calcium, magnesium, selenium, and vitamins A, C, D, and E. Nutritional deficiencies in obesity are mainly caused by poor-quality diets, higher nutrient requirements, alterations in micronutrient metabolism, and invasive obesity treatments. The current conventional agricultural system is designed for intensive food production, focusing on food quantity rather than food quality, consuming excessive agricultural inputs, and producing nutrient-deficient foods, thus generating severe health and environmental problems; agricultural food products may worsen obesity-related malnutrition. Therefore, modern agriculture is adopting new biofortification technologies to combat micronutrient deficiencies and improve agricultural productivity and sustainability. Biofertilization and nanofertilization practices are increasingly used due to their efficiency, safety, and reduced environmental impact. Biofertilizers are preparations of PGP-microorganisms that promote plant growth by influencing plant metabolism and improving the nutrient uptake, and nanofertilizers consist of synthesized nanoparticles with unique physicochemical properties that are capable of increasing plant nutrition and enriching agricultural products. This review presents the current micronutrient deficiencies associated with obesity, the modern unsustainable agri-food system contributing to obesity progression, and the development of bio- and nanofertilizers capable of biofortifying agri-food crops with micronutrients commonly deficient in patients with obesity.