The formation of metallo-pigmentation and copigmentation as potential mechanisms of inking formation was investigated in peach and nectarine skin tissues. Cyanidin-3-glucoside, the most abundant anthocyanin in peaches and nectarines, formed very purple ferric complexes with an anthocyanin/iron molar ratio of two. Greenish metallo complexes between ferric ion and chlorogenic acid, caffeic acid, catechin, or epicatechin formed with an phenolic/iron molar ratio of one. The lack of copigmentation pointed out the importance to focus research on the metallo-phenolics reaction. High intensity of dark color formation was developed with cyanidin-3-glucoside, followed by caffeic acid, chlorogenic acid, catechin, and epicatechin on an equal molar basis. Citric acid acted as a strong iron chelator to prevent and reverse the formation of ferric cyanidin-3-glucoside complexes. The variety of dark and light colored spots observed on the surface of peaches and nectarines is explained by the formation of metallo-pigment complexes.