Post-harvest storage of fleshy fruit is a strategy used for improving seed quality. The aim of this study was to evaluate post-harvest storage of the fruit of C. baccatum var. baccatum (cumari pepper) and relate it to antioxidant enzyme activity and seed physiological potential. Red-colored fruit (65 days after anthesis) was gathered and stored at 20 °C for 0, 5, 10, 15, and 20 days. The seeds were removed and evaluated for moisture content, physiological quality, antioxidant enzyme activity, and protein content. The means were fitted to regression equations and then passed through multivariate analysis (PCA). Seed moisture and 100-seed weight decreased through post-harvest storage. The 5- and 10-days storage periods led to an increase in the germination. Electrical conductivity was greater for the 0- and 20-day storage periods. Dry matter and protein increased in the 5- and 10-days. Enzymes exhibited reductions of activity comparing 0 and 20 days. The post-harvest storage of C. baccatum fruit for 5 and 10 days improves seed physiological potential and is related to physiological maturity. The incomplete maturation of cumari seeds obtained from unstored fruit (0 days) is related to greater enzyme activity, greater oxidative stress, and low germination and vigor. The lack of post-harvest storage of fruit and storage of fruit for longer than 10 days contributes to a lower physiological potential of cumari pepper seeds.