Less common tropical fruits have been the subject of little research, leaving a vast field to be explored. In this context, a comprehensive study was carried out on the bioactive compounds and antioxidant capacity of 51 non-traditional fruits consumed in Ecuador. Vitamin C, organic acids, carotenoids, and phenolic compounds were evaluated using microextraction and rapid resolution liquid chromatography (RRLC) techniques, while antioxidant activity was measured using microplate readings. The results showed high levels of vitamin C (768.2 mg/100 g DW) in Dovyalis hebecarpa, total organic acids (37.2 g/100 g DW) in Passiflora tripartita, carotenoids (487.0 mg/100 g DW) in Momordica charantia, phenolic compounds (535.4 mg/g DW) in Nephelium lappaceum, Pourouma cecropiifolia (161.4 µmol TE/g DW) and Morus alba (80.5 µmol AAE/g DW) in antioxidant activity. Effective extraction of carotenoids was also observed using a mixture of methanol: acetone: dichloromethane (1:1:2) with an extraction time of 2 min, while an 80% solution of 0.1% acidified methanol with hydrochloric acid with an extraction time of 3 min was highly effective for phenolics in fruit. These results provide a valuable basis for optimising future extraction processes of bioactive compounds from non-traditional fruits, with significant implications for their potential use in various nutritional and pharmaceutical contexts.