Few studies investigated low molecular mass aliphatic organic acids (AOA) and amino acids in honey mainly due to their low concentrations in this product. However, these compounds influence the physical, chemical, sensorial, and biological characteristics of honey and their investigation by validated methods are important to guarantee the veracity of these data. Thus, this study aimed to validate a simultaneous method for determination of 13 AOA and two amino acids in floral honey using a capillary electrophoresis system equipped with diode array detector. The proposed method was validated based on Eurachem and Ministry of Agriculture, Livestock, and Food Supply Guidelines, which showed good results for the evaluated validation parameters: system suitability, limits of detection and quantification, linearity, matrix effect, precision, and accuracy. Also, the Peakmaster ® software was used to select an appropriate internal standard. The validated method was then employed to determined AOA and amino acids in multifloral honeys, in which citric, glycolic, gluconic, and glutamic acids were quantified in all samples. Therefore, the proposed method can be used in the determination of AOA and amino acids in floral honeys with precision and accuracy ensured.