3- N -trimethylaminopropionic acid (β-alanine betaine) and trimethylamine (TMA) are important nitrogenous compounds that perform fundamental roles in biological pathways throughout all kingdoms of life; however, yet their simultaneous determination method is hardly reported. Capillary electrophoresis method for the simultaneous determination of TMA and β-alanine betaine in microbial culture and plant samples was developed. To increase the sensitivity, TMA and β-alanine betaine in the samples were first derivatized with bromophenacyl bromide and then analyzed by capillary electrophoresis under low pH. The derivatization was found to be practically useful for the elimination of interfering substances from plant and microbial extracts, as well as giving well resolved peaks for the analytes (β-alanine betaine esters and TMA salt). Analytical features of the developed method showed its respectable performance in terms of linearity ( r 2 > 0.99), precision (relative standard deviation (RSD) < 5%), and detection limits (0.01 mM). The developed method allows the quantitative determination of TMA and β-alanine betaine in complex biological samples and assists to study biosynthetic and degradation pathways of these important compounds.