The current study was designed to characterize the metabolite profile and bioactivity of two commercial bitter melon (Momordica charantia Linn.) genotypes. UPLC-high resolution mass spectrometry (HRMS) was used to identify 15 phenolic and 46 triterpenoids in various bitter melon extracts. Total phenolic levels were the highest (57.28 ± 1.02) in methanolic extract of the inner tissue of Indian Green cultivar, which also correlated to the highest DPPH radical scavenging activity (30.48 ± 2.49 ascorbic acid equivalents (mg of AAE)/g of FD). In addition, highest levels of total saponins were observed in chloroform extract of the Chinese bitter melon pericarp (75.73 mg ± 4.67 diosgenin equivalents (DE)/g of FD). Differential inhibition of α-amylase and α-glucosidase activity was observed in response to polarity of extract, cultivar and tissue type. These results suggest that consumption of whole bitter melon may have potential health benefits to manage diabetes.