Chilling injury (CI), which causes seed browning in pepper, may arise following long-term cold storage, and is a major cause of postharvest losses. To explore potential strategies of minimizing the associated postharvest losses, the present study investigated the optimal pepper harvest time that could reduce levels of seed browning, in addition to the relationship between fruit maturity and seed browning. Fruit harvested 15 days after flowering (DAF) were sensitive to cold storage at 4°C and exhibited 100% seed browning (CI index, 4.0); in contrast, the seed browning rate of fruit harvested 35 DAF was 10% (CI index, 0.4) within 7 d of cold storage. Seed antioxidant activity was higher in seeds harvested at early stages (15 DAF to 20 DAF) than in seeds harvested at later stages (40 DAF to 50 DAF) at the beginning of storage. Pericarps of fruit harvested at 50 DAF exhibited the highest antioxidant activity. Lipoxygenase, catalase, and peroxidase activity, and the expression levels of cell wall-related genes, pectin methylesterase-like protein, and endo-β-1,4-glucanase were higher in seeds of immature fruit harvested 15 DAF than in seeds of mature fruit harvested 35 DAF. The endosperm separated from the seed coat in fruit harvested 35 DAF and the seeds did not brown under low-temperature storage. The lack of seed browning observed in mature fruit under low-temperature storage could be attributed to physical protection provided by the seed coat rather than cold stress resistance conferred by antioxidants.