Peppers are one of the most widely processed and consumed vegetables in the world. The present study was established to obtain phenolic profiles of two fresh and oven-cooked pepper cultivars, red hot Aleppo (Capsicum annuumL.) and red sweet pepper Capia (Capsicum annuumL.). Phenolic extracts of pepper samples have been, for the first time, qualitatively and quantitatively examined by liquid chromatography including tandem mass spectrometry (LC-MS/MS). Apart from the main objective, samples were also examined for their colour alteration regarding the oven cooking process. A total of 20 phenolic compounds were identified and quantified in the red pepper samples. The revealed results showed that the hot Aleppo pepper possessed a much higher phenolic content when compared to Capia peppers. In the Aleppo pepper samples, capsaicin, luteolin 6,8-di-C-hexoside, luteolinO-malonylpentosyldihexoside, luteolin 6-C-hexoside, dihydrocapsaicin, and kaempferol pentosyldihexoside were the most dominant phenolics, while luteolinO-(aposylmalonyl)glucoside, luteolinO-malonylpentosyldihexoside, kaempferol pentosylhexoside, and feruloyl hexoside were for the Capia samples. In the Aleppo samples, capsaicin and dihydrocapsaicin were compounds that significantly increased due to the cooking process. The cooking process not only positively affected the phenolic profile of pepper samples but also the colour, total phenolic content, and antioxidant activity.