The use of improved soybean varieties is crucial when it comes to the progress of soybean cultivation in Indonesia. This study presents the agronomic performance, seed chemical composition, and bioactive components of 12 soybean genotypes grown in Malang, Indonesia. Parameters included the agronomic characteristics, ash, protein, fat, total flavonoid content (TFC), total phenolic content (TPC), genistein and daidzein contents as well as antioxidant activity. The study found that Dena 1, Dering 1, and Deja 1 had the highest seed yield (2.76–2.84 t/ha), while Dega 1 had the largest seed size (24.69 g/100 seeds). The black-seeded genotype of Detam 1 had the highest protein content (39.79% dw), while GH 63 had the largest amount of total daidzein and genistein. Detam 4 (a black-seeded genotype) exhibited the highest values of TFC, TPC, and antioxidant activity. The agronomic characteristics and TPC significantly correlated, suggesting that both traits are applicable as criteria for soybean breeding selection. Detam 4 and GH 63 are likely promising to be used as gene sources for improving the nutritional and health benefits of soybean genotypes. GH 63 and GH 73 also have the potential for further release as new high-yielding varieties with early maturity and large seed size. Overall, the study provides valuable information on the agronomic superiority and nutritional aspects of improved soybean varieties in Indonesia.