A separation method was developed in order to quantify free amino acids in passion fruit juices using CE-UV. A selective derivatization reaction with FMOC followed by MEKC analysis was chosen due to the highly interconnected mobilities of the analytes, enabling the separation of 22 amino acids by lipophilicity differences, as will be further discussed. To achieve such results, the method was optimized concerning BGE composition (concentrations, pH, and addition of organic modifier) and running conditions (temperature and applied voltage). The optimized running conditions were: a BGE composed by 60 mmol/L borate buffer at pH 10.1, 30 mmol/L SDS and 5 % methanol; running for 40 min at 23°C and 25 kV. The method was validated and applied on eight brands plus one fresh natural juice, detecting 12 amino acids. Quantification of six analytes combined with principal component analysis was capable to characterize different types of juices and showed potential to detect adulteration on industrial juices. Glutamic acid was found to be the most concentrated amino acid in all juices, exceeding 1 g/L in all samples and was also crucial for the correct classification of a natural juice, which presented a concentration of 22 g/L.