An enhanced method for the determination of organic acids in several fruit juices by capillary zone electrophoresis (CZE) with direct UV–Vis detection has been developed in this work. First, a study with simulated real juice samples was done to find the best separation conditions. Next, several commercial fruit juices were analyzed, and the organic acid contents were quantified in less than 12 min using a poly(vinyl alcohol)-coated fused-silica ‘bubble cell’ capillary. The present method is reliable, fast and provides detection limits comprised between 0.1 and 2.5 μg mL−1. Moreover, different chemometric techniques, based on CZE data, were examined. Linear discriminant analysis allowed the differentiation of fruit juices according to the fruit type, whereas multiple linear regression models predicted the percentages of orange and pineapple juices in binary blends with grape. Thus, the present methodology is of utmost interest for routine and quality control purposes in food industries.