Abstract Aliphatic organic acids (AOA) make a strong contribution to flavor, taste, acidity, pH and electrical conductivity. In this paper, a new and fast capillary electrophoresis method was developed and validated to determine 14 AOA simultaneously in bracatinga (Mimosa scabrella Bentham) honeydew honey and floral honey. Separation of fourteen compounds occurred in 9 min using glyoxylic acid as an internal standard, and the background electrolyte was comprised of phthalic acid (20 mmol L−1,) Tris (14 mmol L−1), CTAB(1.6 mmol L−1), CaCl2 (1 mmol L−1), pH 3.3. The performance and fitness-for-purpose of this method were assessed based on the results obtained for the parameters: system suitability, linearity, matrix effects, selectivity, precision, accuracy, detection and quantification limits, and robustness. Gluconic acid was the main acid in both kinds of honey. Malonic and glycolic acids were quantified in honeydew honey and floral honey for the first time, while lactic acid was quantified for the first time in honeydew honey.