The present work is aimed to develop and validate a simple, rapid and cost-effective CE method for the determination of trimethylamine (TMA) from bacterial origin. Optimum Sseparation of TMA from the other components of the bacterial culture was achieved in less than 1.1 min using a fused silica capillary (27 cm × 75 μm ID) and a background electrolyte solution that consisted of formic acid (0.75 M at pH 2.05). Analytical characteristics of the proposed method The proposed method was validatedwere evaluated through the study of by testing its specificity, linearity, precision, accuracy, recoveryrobustness, and detection limit/quantitation limit values.The method was linear over the range 25-2000 M (R 2 = 0.999864). The LOD and LOQ were 9 µM and 27 µM, respectively. Intra-day and inter-day RSD were ⩽0.24% and ⩽1.3% for migration time, respectively. Intra-day and inter-day RSD for peak area were ⩽2.44% and ⩽3.51%, respectively. The method showed a good accuracy with recovery percentages ranging from 95.45% to 102.21%. The validated method was successfully applied for the determination of microbial conversion of L-carnitine to TMA. The method shows great potential in highthroughput screening applications to assess the functionality of the gut microbiota to produce TMA.