Purple corn (Zea mays L.) is native to the Andean region, but limited research has been performed about the potential metabolic variability when grown under Andean environmental conditions. This study was aimed at evaluating the phenolic and primary polar metabolites composition of purple corn (kernels and cobs) grown at two Peruvian Andean locations (lowland and highland) using targeted UHPLC (ultra-high-performance liquid chromatography) and un-targeted GC-MS (gas chromatography mass spectrometry) metabolomic platforms, respectively. Changes in the physical characteristics and the in vitro bioactivity were also determined. Purple corn from the highland zone showed higher contents of ash, crude fiber, total phenolic contents, DPPH (2,2-diphenyl-1-picrylhydrazyl) antioxidant capacity, and α-amylase inhibitory activity in kernels, whereas increased levels of flavonoids (anthocyanins and quercetin derivatives) and ABTS [2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)] antioxidant capacity were observed in cobs in comparison to lowland samples. No effect of the Andean location was found on the α-glucosidase inhibitory activity relevant for hyperglycemia management, while yield-linked physical characteristics were high in purple corn grown at the lowland zone. Polar primary metabolites related to the carbohydrate (monosaccharides, sucrose, and D-sorbitol), amino acid (valine and alanine), and tricarboxylic acid cycle (succinic, fumaric, and aconitic acid) metabolism were higher in highland purple corn (cob and kernel) likely due to abiotic stress factors from the highland environment. This study provides the foundation for further breeding improvements at Andean locations.