The phenols and fatty acids profile and in vitro antioxidant and hypoglycaemic activity of seed, peel, pulp or pulp plus seeds of Colombian fruits from Solanaceae and Passifloraceae families were investigated. Ultra-High Performance Liquid Chromatography (UHPLC)-High Resolution Mass Spectrometry (HRMS) revealed the presence of chlorogenic acid as dominant phenolic compound in Solanaceae samples. Based on Relative Antioxidant Score (RACI) and Global Antioxidant Score (GAS) values, Solanum quitoense peel showed the highest antioxidant potential among Solanaceae samples while Passiflora tripartita fruits exhibited the highest antioxidant effects among Passifloraceae samples. P. ligularis seeds were the most active as hypoglycaemic agent with IC50 values of 22.6 and 24.8 g/mL against -amylase and -glucosidase, respectively. Considering that some of the most promising results were obtained by the processing waste portion, its use as functional ingredients should be considered for the development of nutraceutical products intended for patients with disturbance of glucose metabolism.