Deficiency in calcium, zinc, selenium, and iodine remains a major health issue in Africa. A selenium (Se) status survey conducted in central Kenya highlands revealed a high risk of dietary Se deficiency. This study investigates the effect of soil and foliar Se fertilizer application on Se concentration in maize and bean grains. It further tests the combination of Se fertilizer with phosphorus and nitrogen fertilizers, and with zinc and iodine fertilizers. Selenium fertilization results in a significant increase in Se concentration in grains. For the soil application, Se concentration increases on average by 3 µg kg−1 in maize and by 10 µg kg−1 in beans, for each gram of Se applied as sodium selenate. Foliar Se fertilization is more effective and increases Se concentration in grains on average by 18 µg kg−1 in maize, and by 67 µg kg−1 in beans. Total soil phosphorus/availability appears as an important factor influencing soil Se availability. Addition of phosphorus fertilizers positively affects the impact of Se fertilization in locations with low soil P, Fe, and Al. A Se + Zn + I fertilizer combination does not affect the impact on Se concentration in grains. Fertilizing beans alone is found to be more efficient compared to fertilizing only maize. In locations at high risk of dietary Se deficiency, foliar application at 10 g Se ha−1 on beans or 31 g Se ha−1 on maize is sufficient to achieve adequate daily dietary Se intake. The study points towards a multi-mineral agronomic biofortification, based on a site-specific biofortification strategy.