Seed aging is a critical process during storage and plays an important role in maintaining seed vigor. The present study aimed to investigate the effects of seed storage on germination and the differential abundance of proteins associated with viability loss in Cariniana legalis (Mart.) O. Kuntze. Seeds were stored for 12 months at 6 °C in plastic bags. Analyses of germination were performed at time 0 (newly harvested seeds) and after 3, 6, and 12 months of storage. To identify differentially abundant proteins, two-dimensional electrophoresis was performed, followed by tandem mass spectrometric (MS/ MS) analysis. Germination, the germination speed index and the moisture content were significantly reduced during storage. Proteomic analysis revealed 50 differentially abundant proteins among the times analyzed; these proteins were classified into several functional classes related to the biological, metabolic, cellular, oxidation-reduction, carbohydrate metabolism, storage, aging, cell wall organization or biogenesis, response to stress and stimulus, and proteolysis categories. The correlation between seed aging and proteome changes suggests that specific proteins may be involved in the mechanisms underlying seed deterioration, including ferritin, seed maturation-like, 2,4-dienoyl-CoA reductase, 11S globulin, polygalacturonases, superoxide dismutase, heat shock proteins, and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Our data showed that increasing storage time significantly reduced germination and revealed the regulation of differentially abundant proteins, which may be related to the reduction in seed viability in C. legalis.