In this study, the effect of dehydration of some physico-chemical characteristics, total phenol, flavonoids, antioxidant capacity and phenolic compounds of green and red jalapeno pepper fruits was investigated. The total carotenoid contents of red and green jalapeno pepper samples were reported to be between 14.15 (fresh) and 129.00 μg/g (540 and 720 W) to 2.8 (fresh) and 27.25 μg/g (720 W), respectively. Total phenolic results of red and green jalapeno pepper samples were recorded between 205.83 (fresh) and 343.93 mg GAE/100 g (540 W) to 81.69 (fresh) and 309.88 mg gallic acid equivalent (GAE)/100 g (air drying), respectively. The highest decrease in L* results (brightness) of both red (32.33) and green (36.45) peppers was determined with air drying. Gallic acid, catechin and kaempferol were the predominant phenolic compounds of jalapeno peppers. Gallic acid amounts of red and green jalapeno pepper samples changed between 3.23 (fresh) and 16.20 mg/100 g (air) to 2.41 (fresh) and 9.30 mg/100 g (air), respectively. Also, catechin amounts of both red and green dehydrated jalapeno pepper fruits were determined between 3.24 (fresh) and 106.33 mg/100 g (900 W) to 2.89 (fresh) and 90.05 mg/100 g (air), respectively. Both conventional and microwave drying has caused the reduction of redness for red pepper and greenness for green pepper. The phenolic components of red jalapeno peppers were partially higher than the green ones.