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Seed coat color is one of the main agronomical traits that determine the chemical quality of soybean seeds and has been used as a parameter during cultivar development. In this study, seeds of yellow (<i>n</i> = 10), greenish-yellow (<i>n</i> = 5), and light-yellow (<i>n</i> = 4) soybean accessions were evaluated for their contents of total protein, total oil, total phenolic (TPC), and five prominent fatty acids including palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), and linolenic acid (LLA), relative to a control cultivar, and the effect of seed coat color on each was investigated. Antioxidant activity was also evaluated using 1,1-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, Trolox equivalent antioxidant capacity (TEAC), and ferric reducing antioxidant power (FRAP). The results showed significant variations of metabolite contents and antioxidant activities between the soybeans. The average TPC, DPPH-radical scavenging activity, and FRAP were each in the order of greenish-yellow > yellow > light-yellow soybeans. In contrast, light-yellow soybeans contained a high level of OA and low levels of SA, LA, and LLA, each except LA differing significantly from yellow and greenish-yellow soybeans (<i>p</i> < 0.05). Our findings suggest that greenish-yellow and light-yellow soybeans could be good sources of antioxidants and high-quality soybean oil, respectively.