Surface properties of nanomaterials are important characteristics influencing the in vivo fate. Today, the most common parameter considered while characterizing nanomaterial surfaces evaluates their surface charge determining an apparent zeta potential. This zeta potential is deduced from measurement of the electrophoretic mobility of nanomaterials dispersed in aqueous media by well established methods that are described in the standards ISO 13099. Among the different methods, electrophoretic light scattering (ELS) is used in routine in many laboratories, but no validated protocols were proposed so far. This paper was aimed to propose a standardization of a protocol for evaluating zeta potential of nanomaterials by ELS and a methodology to achieve its validation. The robustness, precision and trueness were investigated using reference materials including positive and negative standards. To assess the robustness, experimental factors that could influence results from measurements of zeta potential were considered. These included the batch of measurement cells, the temperature of sample, the type of measurement cells and the analyst giving reliability of protocol for normal usage. Specifics methods of nested designs were developed to investigate robustness and precision and interpret the results using analysis of variance ANOVA. The estimation of the contribution of each factor to the total variance using the estimated mean square values and the equations for expected mean square was used to interpret the ANOVA table. When this method could not be used because of the obtaining of a negative value of the variance, the method based on pooled variances was used to interpret the ANOVA table. The proposed protocol was found robust, accurate and consistent with standard ISO. Uncertainty of the protocol were 14 and 12 % for nanomaterials of negative and positive charges respectively proving reliability of results and approving the validity of the protocol used.