Peruvian corn biodiversity is one of the highest in the world and may represent an important natural source of health relevant phenolic bioactive compounds whose potential needs to be investigated. This study investigated twenty-two Peruvian corn samples corresponding to five corn races (Arequipeño, Cabanita, Kculli, Granada and Coruca) in relation to their total phenolic contents (TPC), anthocyanin contents, Ultra-Performance Liquid Chromatography (UPLC) phenolic profiles and antioxidant capacity (ABTS and ORAC methods). Subsequently using both free and cell-wall bound phenolic fractions their health relevance targeting hyperglycemia (α-glucosidase and α-amylase inhibition) and obesity (lipase inhibition) potentials was evaluated using in vitro assay models. Antioxidant capacity and TPC were high in bound fractions from yellow-colored races in contrast to the purple-colored race (Kculli) which had high TPC (mainly anthocyanins) and antioxidant capacity in the free form. The major phenolic acids detected by UPLC were ferulic and p-coumaric acids. High α-glucosidase (32.5–76.1%, 25 mg sample dose) and moderate α-amylase inhibitory activities (13.6–29.0%, 250 mg sample dose) were found in all free fractions, but only samples from the Kculli race had lipase inhibitory activity (58.45–92.16%, 12.5 mg sample dose). Principal component analysis revealed that the variability of data was affected by the race and the α-glucosidase and lipase inhibitory activities positively correlated with anthocyanins and antioxidant capacity. Some accessions of Kculli, Granada and Cabanita races are promising for future breeding strategies focused on the development of improved corn varieties targeted for the design of functional foods relevant for hyperglycemia and obesity prevention.