Fruit juices are naturally acidic, and the acidity is due to the formation of various organic acids formed in several metabolic processes. The content of acids varies due to various processing parameters during the preparation of fruit juices and their packaging for commercialization. Quantitative determination of organic acids provides the necessary information leading to changes occurred during processing. The organic acids were extracted by ion-pair dispersive solid-phase extraction by multiwalled carbon nanotubes and analyzed using gas chromatography-mass spectrometry (GC-MS) and in situ butylation. The developed analytical method was validated, and the obtained results showed a linearity in the range of 0.5-5000 μg/L levels of the analytes with limit of detection and quantification values of 2-10 and 5-20 μg/L, respectively. The inter- and intra-day reproducibilities are less than 15% with 80%-98% recoveries and less than 20% matrix effect. The developed method was used for the quantitative determination of organic acids present in fresh and packaged apple, grape, orange, and pomegranate juice samples. The content of organic acids was observed in the range of 0.26-3793 μg/L. Pimelic acid was not detected in any of the analyzed fruit juices. Fumaric acid (FA) was observed to be a major organic diacid present in the natural fruit juices. The results indicated that the processing of fruit juices for packaging decreases the content of organic acids in fruits. The developed GC-MS-based analytical method for the analysis of organic acids has good sensitivity and reproducibility for the quantitative determination of various organic acids in fruit juices. FA was observed to be the major carboxylic acid present in fruits. The processed juice samples possess the lowest concentration of organic acids, suggesting that processing has a significant effect on the concentration of organic acids in fruits.