In this work, the main organic acids (citric, malic and ascorbic acids) and sugars (glucose, fructose and sucrose) present in commercial fruit beverages (fruit carbonated soft-drinks, fruit nectars and fruit juices) were determined. A novel size exclusion high performance liquid chromatography isocratic green method, with ultraviolet and refractive index detectors coupled in series, was developed. This methodology enabled the simultaneous quantification of sugars and organic acids without any sample pre-treatment, even when peak interferences occurred. The method was in-house validated, showing a good linearity (R > 0.999), adequate detection and quantification limits (20 and 280 mg L−1, respectively), satisfactory instrumental and method precisions (relative standard deviations lower than 6%) and acceptable method accuracy (relative error lower than 5%). Sugars and organic acids profiles were used to calculate dose-over-threshold values, aiming to evaluate their individual sensory impact on beverage global taste perception. The results demonstrated that sucrose, fructose, ascorbic acid, citric acid and malic acid have the greater individual sensory impact in the overall taste of a specific beverage. Furthermore, although organic acids were present in lower concentrations than sugars, their taste influence was significant and, in some cases, higher than the sugars’ contribution towards the global sensory perception.