The effect of processing conditions (temperature and degree of polymerisation, DP) on the stability of short-chain fructooligosaccharides (sc-FOS) was investigated in three reaction media (sodium citrate buffer and orange and tomato juices) in a kinetic study at pH 3.5. In addition, kinetic equations as a function of temperature and pH were developed, using published data. Pentasaccharides were more stable to heat treatment than were trisaccharides under all of the conditions tested. In addition, the sc-FOS were more stable in orange juice, followed by tomato juice and citrate buffer. The results showed that, in addition to temperature and pH, the DP and food matrix, including the type of pasteurisation, must be considered when processing foods enriched with sc-FOS. Furthermore, the continuous thermal processing simulation for each of the equivalent processes at 90°C revealed that the percent retention of sc-FOS is greater than 95% at temperatures above 95°C.