Soybeans contain flavonoids and anthocyanins that are associated with health benefits related to antioxidant activities. In this study, the total flavonoid content (TFC), total anthocyanin content (TAC), and the relative antioxidant activities (AOA) of selected Philippine soybean genotypes were screened in order to select and recommend promising genotypes that may be used for further breeding and varietal development. Using the aluminum trichloride method, the genotypes POP 1-44 (TFC = 0.619 g/100 g), PHL 29272 (TFC = 0.616 g/100 g), and Tiwala 6 (TFC = 0.608 g/100 g) were determined to have the highest calculated TFC values. pH differential and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays distinguished all three black-seeded soybean genotypes PHL 29272 (TAC = 177.010 mg/100 g; AOA = 24.476%), PHL 29502 (TAC = 143.750 mg/100 g; AOA = 25.745%), and PHL 29552 (TAC = 123.572 mg/100 g; AOA = 29.297%) with the highest anthocyanin contents and relative antioxidant activities. Genotype PHL 29272 was consistently found among those with the highest results for the three tests. Significant correlations (α = 0.05) were found between flavonoid content and antioxidant activity (p < 0.0001), and between anthocyanin content and antioxidant activity (p < 0.0001). In conclusion, the study was able to identify genotypes that can be recommended as the most suitable candidates for soybean breeding activities.