A novel HPLC method has been established for the determination of thiols in fruit samples, introducing, for the first time, methyl propiolate as an advantageous precolumn derivatization reagent for cysteine (CYS), glutathione (GSH), and N-acetylcysteine (NAC). The formed derivatives were detected at 285 nm, following isocratic separation on a core-shell column (Ascentis Express C18, 50 × 2.1 mm i.d., 2.7 μm) with a mobile phase of 15 mmol L−1 (ΝΗ4)2ΗPO4/H3PO4 (pH = 2.2)/methanol (92:8 v/v), containing 1 mmol L−1 EDTA, at a flow rate of 0.2 mL min−1. Derivatization parameters were optimized including pH and concentration of buffering medium, amount concentration of methyl propiolate, derivatization time, and temperature, by the univariate approach. Under optimal conditions, the developed analytical scheme offers a total analysis time of less than 10 min, limits of detection in the range 0.1–0.5 μmol L−1, and satisfactory linearity up to 100 μmol L−1 for all analytes. The method proved also to be equally selective and robust. Endogenous thiols were determined in melon, watermelon, and avocado, using the standards addition approach, after minimal sample preparation, with no use of organic solvents. The accuracy was evaluated by recovery experiments resulting in the range of 86.4–118.5 %.