Chili peppers have been under the spotlight of bioactivity research as they feature a diverse and rich phytochemical profile with multiple health promoting effects. These beneficial properties are related to the chemical composition of chili peppers and is of utmost importance to identify varieties with the strongest bioprospecting potential. In this study, 19 chili pepper varieties were investigated originating from Capsicum annuum L. (n = 3), Capsicum baccatum L. (n = 3) and Capsicum chinense Jacq. (n = 13) species. Firstly, a suspect screening based on a spectral library was applied and the bioactive profile of all samples was acquired using ultra-high-performance liquid chromatography hybrid quadrupole time-of-flight mass spectrometry (UHPLC-q-TOF-MS). The ethanolic extracts were richer in bioactive compounds and exhibited the highest antioxidant capacity. Then, 6 different enzyme assays were performed targeting enzymes involved in non-communicable diseases, such as cholinesterases involved in Alzheimer's disease or pancreatic lipase in obesity. The strongest inhibitory effect was noticed for 6 Capsicum chinense Jacq. varieties (half maximal inhibitory concentration ranging between 0.56 and 9.2 mg/mL), namely Moruga, Naga chocolate, Bhut jolokia, Carolina reaper, Trinidad scorpion moruga and Naga morich. By using the enzyme inhibitory profile, it was feasible to discriminate these 6 varieties from the rest tested based on a principal component analysis (PCA) model. Moderate and strong correlations were also noticed between the relative content of the identified compounds and the enzyme inhibition. Naringenin, a flavanone, and vanillic acid, a phenolic acid, strongly correlated towards human acetylcholinesterase and alpha glucosidase inhibition, respectively. Overall, the presented results underscore the high potential of Capsicum chinense Jacq. species to be used as sources of bioactive natural compounds for nutraceutical applications.