Differences in seed storage tolerance between soybean cultivars have been frequently observed. Thus, identifying compounds found in them that may be related to these differences is necessary to support the selection of cultivars with seeds with better storage potential. Therefore, this study aimed to evaluate changes in viability and vigor of soybean seeds during storage in two environments, relating them to antioxidant activity, production of reactive oxygen species, and metabolites of the phenylpropanoid pathway. The experimental design was completely randomized in a 4 × 5 factorial scheme (storage periods × cultivars). Cultivars with contrasting characteristics of lignin content, seed coat color, and isoflavone content in the seed were used, stored for six months in a cold and dry chamber and an uncontrolled environment. Every two months, viability and vigor, enzymatic activity (superoxide dismutase and catalase), and hydrogen peroxide content were evaluated. Storage in a cold and dry chamber maintains seed viability of cultivars A, C, and D; it is reduced in all cultivars in an uncontrolled environment. Seed vigor is reduced during storage. There is no association between the seeds' physiological quality and the superoxide dismutase and catalase activities. The increase in the hydrogen peroxide content in the seed coat is an indicator of the reduction in the seed physiological quality when stored in an uncontrolled environment. The difference in deterioration tolerance during storage is associated with the lignin content in the seed coat.