The dual-stage sugar substitution (D3S) method was used to incorporate isomaltulose into banana slices. In the first stage of the technique, native fruit sugars were partially removed and, in the second, isomaltulose, a carbohydrate with a low glycemic index, was incorporated into the banana slices. Ultrasonic energy was applied to one or both stages in order to evaluate its influence on the process. Samples subjected to ultrasonic waves (40 kHz) in both stages presented greater water losses (10.007 ± 0.554%) and greater solids gains (4.809 ± 0.195%). The D3S process resulted in longer drying times of the banana slices. The mathematical models used to describe the drying process showed good adjustment, with emphasis on Midilli's (R² > 0.999). The application of the D3S method without ultrasound energy resulted in dried samples with greater longitudinal shrinkage, radial shrinkage, shrinkage coefficient and greater differentiation in terms of color compared to the other treatments. The use of ultrasonic energy in both stages of the method results in better physicochemical characteristics of the final product. Samples subjected to the D3S process showed a lower rehydration capacity.