Introduction Carbohydrates are important constituents in fruits. Among the carbohydrates, disaccharides have rarely been studied in apple and peach. Indeed, the abiotic stress biomarker and preservation agent α,α-trehalose is a disaccharide. Objectives To establish a comprehensive method based on two-dimensional gas chromatography combined with time-of-flight MS detection (GC × GC–ToF/MS) to analyse the disaccharide composition of apple and peach. Methods The sample preparation was based on aqueous-methanolic extraction of the analytes, followed by oxime formation and trimethylsilylation of the disaccharides. First, three columns were tested with standards on the one-dimensional system. Next, to perform the sample analysis using GC × GC–MS (which offers significant advantages over conventional GC because it allows higher separation efficiencies), various column configurations were assessed on the two-dimensional system to obtain enhanced separation and low detection limits. The column sets tested included non-polar/semi-polar, semi-polar/polar and polar/non-polar. Results Using the method that proved to be more efficient, namely the method developed with the semi-polar/non-polar configuration, ten disaccharides were identified, based on analytical standards, retention index and mass spectra. These compounds were quantified in several varieties of apple and peach fruit using the developed GC × GC method and linear curve calibration, resulting in substantial differences among the fruits. However, cultivars within the fruits exhibited no significant differences. Conclusion The proposed method allowed for the identification and quantification of several disaccharides in apple and peach, including the biomarker α,α-trehalose.