An innovative protocol for the fast analysis of some organic acids in red wine by co-electroosmotic capillary zone electrophoresis and indirect UV detection using hexadimethrine bromide (HDB) as coating agent was proposed. The adsorption of HDB onto the capillary wall provided a stable electroosmotic flow and separation of small anions was carried out using background electrolytes containing no polymer additive. Low RSD% values (<3.6%) in terms of migration times and effective mobilities were obtained from the analysis of a mixture of nitrate and nitrite and of a mixture of organic acids. An experimental design approach was used to investigate the effects of temperature, separation voltage, and percentage of methanol added to the running buffer solution on the separation of the analytes. A faster method allowing the separation of the organic acids involved in the malolactic fermentation of wine was developed. Using a running electrolyte consisting of 35% (v/v) methanol in a solution of 22 mM benzoic acid at pH 6.10 adjusted with 1.0 M TRIS-base buffer, the separation of tartaric, malic, succinic, acetic, and lactic acids was feasible in less than 210 s. Application of the method to the quantification of the above-mentioned organic acids in Italian red wine samples is reported.