In this study, we investigated the control of western flower thrips [Frankliniella occidentalis (Pergande, 1895) (Thysanoptera: Thripidae)], which is an important pest in tomato and green pepper growing areas in Turkey, under cold storage conditions with phosphine fumigation. The trials were conducted in Mersin in 2015, due to infestations of F. occidentalis damaging the export quality of tomatoes and green peppers. The experiments were conducted by using ECO2FUME (R) with different phosphine gas concentrations including 500, 1000 and 2000 ppm. Fumigation chambers were kept at 4 degrees C. Lowest mortality was seen at 500 ppm gas concentration with 72% for larval stage on tomatoes and 73.75% mortality for pupal stage on green pepper. The data demonstrate that the minimum requirement of phosphine gas concentration 100% mortality of all stages of F. occidentalis was at 2000 ppm. The quality of treated fruit was investigated by analyzing weight loss, sensory quality, fruit firmness, fruit skin color, total soluble solids, titratable acidity contents, physiological and pathological disorders. After treatment, there were no changes in physiologic, pathological and shelf-life properties of the products. The results indicated that, phosphine is a suitable fumigant at low temperature for disinfestion of F. occidentalis from tomatoes and green peppers before shipment.