Abstract: In this research, sweet Kesan peppers and hot Urfa peppers were blanched in different conditions which were used microwave and water. This application was carried out at different temperatures and time intervals. The samples were frozen at -40 ° C and then stored at -20 ± 2 ° C for 10 months. During this period, storage stability of red peppers with no enzyme activity and different levels of enzyme activity were investigated. Therefore, the aim of this study was to discuss which pre-treatment gives the best result for high quality, usefulness of blanching and differences between varieties. It was found that sweet peppers had a higher peroxidase and lipoxygenase activity than hot peppers. In Urfa peppers which contain a high level of capsaicin having an antioxidant effect, losses of colour compounds for both varieties were found to be lower then that of the sweet peppers. The losses of capsantin in the treatments decreased by decreasing lipoxygenase enzyme activity. Before storage of sweet peppers, vitamin C content (170.20 mg/100 g) decreased to 79.05 mg/100 g (53.52%) in the tenth month. This reduction in Urfa peppers was from 201.62 mg/100 g to 111.75 mg/100 g, which is 44.78%. In samples of non-blanched Urfa peppers, capsaicin content was found to be 56.34 mg/100 g. Before the storage loss of capsaicin was up to 16.08% with blanching at 85 ° C for 4 min. At the end of the storage period, capsaicin content of non-blanched peppers was lower then that of microwave and water-blanched peppers. Higher temperatures and longer time lengths will cause a decreasing in capsantin and vitamin C content, It could be concluded that using lipoxygenase enzyme as an indicator instead of peroxidase enzyme used in 5 min blanching at 85 ° C as a commercial application would help to decrease losses in quality are related compounds in some red peppers.