Given the proscription of using chemicals from synthesis, the alternatives for postharvest management of organic produce are limited. Consequently, great interest is being devoted to develop and optimize alternative postharvest approaches. In this work we tested mild heat treatments for green and red fresh-cut peppers and evaluated their effect on quality maintenance under normal distribution and retail temperatures (4 °C). Pepper sticks (1 × 5 cm) at red and green ripening stages were heat-treated (HT) by immersion in water at 45, 50 or 55 °C (1, 3 or 5 min) and quality maintenance during storage was evaluated. Green peppers were more tolerant to HT than red fruit. Both green and ripe peppers subjected to hot water dips at 45 °C for 3 min showed lower spoilage than the control. The treatments markedly reduced soft rots (2 and 4 fold for red and green fruit respectively). Hot water dips also prevented shriveling, weight loss, color changes and contributed to maintain lower fruit respiration during storage. The treatments did not alter sugar content, acidity or antioxidant capacity. Despite of the effective control of soft rots only a slight reduction of microbial counts (<1 log CFU g⁻¹) was found. This suggests that other responses besides biocide effects or microbial wash-off are involved. The treatments delayed pectin solubilization and softening and prevented membrane leakage. Short mild heat treatments (45 °C, 3 min) may be a simple and appealing non-chemical approach to supplement the benefits of low temperature management, extending the shelf life of organic fresh-cut green and red peppers.