The effects of organic modifiers—alcohols (methanol, isopropanol), acetonitrile, and tetrahydrofuran—and β-cyclodextrins in capillary zone electrophoresis were investigated using a test mixture containing five biogenic amines important from the human health point of view—serotonin, dopamine, adrenaline, noradrenaline, and tyramine—and two B vitamins—thiamine and pyridoxine. The simultaneous addition of tetrahydrofuran and isopropanol was found to improve the resolution of determined analytes and enable effective separation of analytes with very similar electromigration characteristics migrating as one peak (dopamine and serotonin). The developed and optimised separation method based on capillary zone electrophoresis and ultraviolet detection was capable to achieve detection limits at the concentration level in the range of 0.15 to 1.25 μg/mL−1. The developed method was also characterised by other favourable validation parameters, such as linearity (