Abstract A micellar electrokinetic capillary chromatography (MECC) method for the determination of soybean isoflavones in soybean meal and fermented soybean meal was established. The separation was performed on a fused and uncoated silica capillary of 50 μm × 60 cm (50 cm of effective length). A solution of 10 mmol L−1 sodium borate (pH 9.4) containing 15 mmol L−1 sodium dodecyl sulphate (SDS) and 5% (v/v) methanol was used as the running buffer. Under the optimum conditions, the six soybean isoflavones were completely isolated within 25 min and were quantifiable within the linear range of their calibration curves. The average recoveries (n = 5) were 99.6–103.5% and the RSDs were 1.8–2.3% for daidzin, daidzein, genistin and genistein. This method is accurate, reliable, economical, easy to operate and suitable for the determination of soybean isoflavones in soybean meal and fermented soybean meal.