BACKGROUND In recent years, debate on the addition of benzoyl peroxide (BP) to wheat flour has increased in China. Medical studies have so far not confirmed that BP in wheat flour causes definite damage to the human body, but its main metabolite in the human body is benzoic acid. The addition of BP to wheat flour has been forbidden in China since 1 May 2011. It is therefore necessary to develop a suitable method to determine BP in wheat flour. RESULTS A simple method using capillary electrophoresis (CE) was developed for determination of BP in wheat flour. BP was determined as benzoic acid after preceding reduction by potassium iodide. Separation was completed in less than 7 min with a running buffer of 10 mmol L⁻¹ sodium borate (pH 9.18), 4 s hydrodynamic injection, 25 kV separation voltage and UV detection at 228 nm. The method was validated in terms of linearity, sensitivity, detection limit, precision and accuracy. The detection limit was 0.29 µg mL⁻¹. The method was successfully applied to the determination of BP in wheat flour samples, with recoveries between 96.1% and 102.6%. CONCLUSIONS The performance of the CE method was comparable, and the quantitative results were in good agreement with those using high-performance liquid chromatography (HPLC). Meanwhile the proposed CE method has the advantages of better resolution, shorter analysis time and lower cost, and would be a good alternative to HPLC for routine monitoring of BP amount in wheat flour.