Fructooligosaccharides have important potential use in the food industry due to their properties such as solubility in water, stability in acidity of fruit juices and during storage, low-calorie value and prebiotic effects. In this study, for the first time, Zymomonas mobilis levansucrase was used for in situ 6-kestose production in carob molasses. The produced kestose was stable during storage at 20 °C for 4 months. The product was evaluated for color, non-enzymatic browning index and titratable acidity during storage and the quality of the product was found comparable to that of control. Furthermore, the decreased amount of sucrose resulted in the prevention of 5-hydroxymethylfurfural (5-HMF) formation during storage. As a result, carob molasses was converted into a high-quality prebiotic product with decreased sucrose content and reduced 5-HMF quantities, and a new method was developed to prevent 5-HMF formation in fruit juices and molasses.