A fast in-capillary derivatization method by CE with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate was developed for the first time for the determination of amino acid enantiomers (arginine, lysine, and ornithine) in dietary supplements and wines. Because of the initial current problems due to the formation of precipitates into the capillary during the derivatization reaction, a washing step with an organic solvent as DMSO between injections was necessary. Different approaches were also investigated to enhance the sensitivity of detection. A derivatization procedure, where plugs of ACN, derivatizing agent (10 mM 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate), and sample in borate (1:1 v/v) were injected in tandem (2, 3, and 6 s, respectively, at 50 mbar), was selected because it enabled to obtain the most sensitive and reproducible results. Appropriate analytical characteristics (linearity, LOD and LOQ, precision, absence of matrix interferences, and accuracy) were obtained for this method. Finally, the optimized method was successfully applied to the determination of the enantiomers of arginine, lysine, and ornithine in food samples of different complexities (dietary supplements and wines).