Pepper fruits, of Capsicum annuum cv. Padron, undergo changes in content of capsaicinoids, lignin, and free phenolics during the maturation process. Although capsaicinoids increase with development, the maximal levels of free phenolics and lignin are observed during the early stages of development. A decrease of peroxidase activity was observed during maturation, and this was related with a decrease in other physiological parameters studied, namely chlorophylls and pH. Subcellular fractionation studies reveal that most peroxidase activity is localized in the soluble fraction throughout development. The changes in the peroxidase activity were accompanied by changes in the different isoenzymes. Acidic isoenzymes increased whereas the basic isoenzymes decreased over the same period, and the changes in these isoenzymes were related with capsaicin metabolism.