Blue maize is used in the production of various traditional foods, and its phytochemical composition has been claimed to possess health benefits. In this study, two blue maize hybrids with pigmented germ grown in five environments were studied under the hypothesis that the germ could have a different anthocyanin profile from that of anthocyanins synthesized in the aleurone layer, and that those in the germ could increase the total anthocyanin content in the whole grain. The percentage of pigmented germ, total anthocyanin content (TA) and total soluble phenols in the germ, whole grain and tortilla were evaluated to determine how tortilla color is modified. For the first time, the anthocyanin and fatty acid profiles of pigmented germ were determined. In the anthocyanin profile, anthocyanins derived from peonidin stood out, making 50.7 %. The most abundant fatty acid was linoleic acid (40.6 %). Whole kernel TA content increased when the maize had a higher percentage of pigmented germ, with minimal changes when grain was transformed to tortilla, resulting in darker tortillas. The large variation in TA among environments highlights the importance of identifying the environments that most favor anthocyanin synthesis.