The degradation process of fructo-oligosaccharides (Raftilose® P95) has been studied in apple pulp matrix at 70–80 °C in pH range 2.7–3.3. Changes of sugar compositions have been analysed by an appropriate isocratic HPLC with differential refractive index detector for oligosaccharide determination. According to Arrhenius equation significant effect of temperature has been observed on the decrease of oligomer concentration. The oligomers (DP3-DP7) degrade continuously at any pH between 2.7 and 3.3. The lower the pH the higher the change of oligomer and monomer concentration is. The oligomers (DP4-DP7) could give out in 30–40 min below pH 3.0 caused by the high concentration of protons. The rate of degradation depends not only on the processing time, temperature, and the proton concentration of the solution, but on the characteristic of apple pulp, too, where the degradation is significantly higher than that in water solution.