Antifungal activity in lemon and pomegranate peels was considerable against Aspergillus flavus, higher in pomegranate (DIZ 37mm; MIC 135μg/mL). Powdered peels (5, 10, 20% w/w) were mixed in inoculated rice. The inhibitory effect on fungal-growth and production of aflatoxins by A. flavus was investigated at storage conditions – temperature (25, 30°C) and moisture (18%, 21%) for 9months. The maximum total aflatoxins accumulated at 30°C, 21% moisture and at 25°C, 18% moisture were 265.09 and 163.45ng/g, respectively in control. Addition of pomegranate-peels inhibited aflatoxins production to 100% during four month-storage of rice at 25°C and 18% moisture, while lemon-peels showed similar inhibitory effect for 3months at same conditions. However a linear correlation was observed in aflatoxins level with temperature and moisture. Studies showed that both fruit-wastes are potent preventer of aflatoxin production in rice, useful for a safer and longer storage of rice.