Multiple micronutrient deficiency remains a health issue in developing countries. The estimated risk of mineral deficiencies in Africa is highest for Ca, Zn, Se, and I. A Se status assessment survey in the rural central Kenya highlands recently conducted by our research group revealed a high risk of dietary Se deficiency at 87% among under-5 children and 97% among women. Effective strategies are needed to reach these rural communities whose diets depend on subsistence farming. Therefore, this study investigated maize and bean crops’ response to Se fertilization in the central Kenya highlands. The experiment comprises of a soil and foliar Se fertilizer application, based on control, 5, 10, and 20 g Se ha^-1 treatments. The effect of combining Se fertilizer with P and N fertilizers, on Se concentration in grains is evaluated. A full factorial experiment explores further the effect of combining Se fertilizer with Zn and I fertilizers, on Se concentration in the grains. Soil fertilizer application was conducted before sowing and foliar fertilizer application during crop’s stem elongation stage. Compared to the control, Se fertilizer application significantly increases Se concentration in both maize and beans, and increases linearly with increase in Se fertilizer application doses. In the soil application, Se concentration increases on average by 0.008, 0.034, and 0.059 mg kg^-1 in maize grains, and by 0.057, 0.108, and 0.165 mg kg^-1 in bean grains, for the 5, 10, and 20 g Se ha^-1 treatments respectively. The P and N fertilizers have a positive effect on Se concentration in grains. The foliar application results in significantly higher Se concentration in grains, with Se concentration increasing on average by 0.123, 0.171, and 0.272 mg kg^-1 in maize grains, and by 0.353, 0.713, and 1.173 mg kg^-1 in beans. Foliar application is therefore more effective. The effect of Se fertilization varies across the study locations, and is influenced by variation in soil characteristics, weather conditions, and crop species. Crop’s response to Se fertilization is highest in Mbuyu, implying that Se fertilization has more impact in locations at higher risk of dietary Se deficiency. The study infers that, in locations at high risk of dietary Se deficiency, a foliar Se fertilizer application at 10 g Se ha^-1 on beans is sufficient to improve average dietary Se intake to daily requirements among the local population. However, if only maize crops are biofortified, a foliar Se fertilizer application of 20 g ha^-1 will instead be needed. In locations at lower risk of dietary Se deficiency such as Mbeu and Kiaga, soil Se fertilizer application at 10 g ha^-1 on beans crops is sufficient, or foliar Se application below 5 g ha^-1. Combining Se with Zn and I fertilizers does not result in significant interaction effects on Se concentration in grains. Selenium fertilizer treatment is the main variable with a significant large effect on Se concentration in the grains. There is therefore a leeway for a combined Se, Zn, and I agronomic biofortification intervention aimed at addressing the existing multi-mineral deficiencies.