Aroma is one of main factors impacting fruit and vegetables quality and consumer appreciation. Since aroma involves the perception of a pletora of volatile organic compounds (VOCs), their assessment is crucial to guarantee the selection and marketability of high quality fruits. High priority should thus be given to replacing poor flavor cultivars with favorable ones, exploiting the variability already available in nature. However, the analysis of the aroma trait in a large number of samples, necessary to overcome the usually massive biological and genetic variability among samples, may be laborious and time consuming. The application of Proton Transfer Reaction -Time of FlightMass Spectrometry (PTR-ToF-MS) has been recently described and demonstrates that it is a powerful high-throughput phenotyping tool for both genetic and quality related studies. This contribute describes the application of PTRToF-MS for the study of the aroma variability present in the germplasm collection of the main berries species available at the Foundation E. Mach, with particular regard to strawberry (Fragaria x ananassa), raspberry (Rubus), and blueberry (Vaccinium). The rapidity and the moderate cost of PTR-ToF-MS analysis allowed us to perform a detailed aroma characterization of each species with a peculiar attention to the VOC fold changes caused by ad hoc storage experiments tailored to simulate the “from farm to fork” chain. The results obtained in these investigations gave important explanatory information to be implemented in the breeding programs.