A capillary electrophoresis method for selective simultaneous determination and quantitation of native amino acids and lactic acid during cultivation of Lactobacillus helveticus D75 and D76 strains on the MRS-1 and milk nutrient media was presented. The method provided sensitive UV-detection of native analytes with minimum sample preparation and appeared to be extremely useful for the analysis of culture media. Native amino acids and lactic acid were separated and detected as complexes with Cu2+ ions, while proposed application of β-cyclodextrin (β-CD) and its charged and uncharged derivates (sulfated β-CD and 2-hydroxypropyl-β-CD) as pseudo stationary phases provided better separation selectivity. The effect of CDs, Cu2+, sodium acetate, β-CDs concentrations and pH of background electrolyte (BGE) on the electrophoretic mobilities of AAs was thoroughly investigated. The composition of the BGE was found to be as follows: 20 mM acetate buffer solution, 50 mM CuSO4, 10 mM 2-hydroxypropyl-β-CD, pH 4.3. The developed method possessed high analysis-to-analysis and day-to-day repeatability of migration times (RSD ≤ 1.0% and ≤ 2.5%, respectively). The differences in production of amino acids by D75 and D76 strains grown together and separately were found and concluded to be a consequence and/or one of the causes of synergism and syntropy of the strains. The developed method proved to be applicable for the analysis of culture media.