Raw and heat-processed jalapeño peppers (green and red) were evaluated for their pigment profile and antioxidant capacity. Sixty-seven pigments were separated and characterized by HPLC-DAD-MS, including carotenoids (isomers and esters), chlorophylls, and pheophytins. The distinctive characteristics of this pepper genotype were the presence of antheraxanthin monoesters, zeaxanthin monoesters, mutatoxanthin diesters, and a higher content of free capsanthin relative to the mono- and diesterified forms. Chlorophyll a and free all-trans-lutein were the major pigments in raw green peppers, whereas free all-trans-capsanthin was the most abundant pigment in raw red peppers. Twelve compounds were generated by the heat treatments, mainly pheophytins and cis isomers of carotenoids. Heat treatments affected differentially the concentration of individual pigments. Red peppers showed a higher antioxidant capacity than green fruits. Heating caused minor changes in the antioxidant capacity of peppers.