Common beans are an essential food source worldwide, particularly in developing countries, and are grown in soils poor in selenium (Se), a mineral essential for human health. Adding Se to fertilizers is a promising technique; however, more studies are needed on the efficacy of this technique on common beans. This study aimed to evaluate the biofortification utilizing Se-enriched nitrogen fertilizers on common bean seeds’ agronomic, physiological, and nutritional characteristics. The pot experiment used a randomized block design with five treatments (urea, Se-enriched urea, ammonium sulfate, Se-enriched ammonium sulfate, and without N and Se), four genotypes (BRS Cometa, BRS Estilo, BRSMG Madrepérola and Pérola), and three replicates. The highest seed yield was 28.31 g pot⁻¹ with Pérola genotype fertilized Se-enriched ammonium sulfate. Photosynthetic rates ranged from 30.37 to 39.06 µmol m⁻² s⁻¹ for Pérola and BRSMG Madrepérola, both with Se-enriched ammonium sulfate. The highest seed Se concentration was 11.17 µg g⁻¹, with BRSMG Madrepérola fertilized with Se-enriched urea being 22.02%, 17.64%, and 22.47% higher than BRS Cometa, BRS Estilo, and Pérola, respectively. Se-enriched nitrogen fertilizers boost seed yield and alter physiological responses based on genotypes and Se-fertilizer interactions. Se-enriched fertilizers applied to soil can increase the Se concentration in common beans.