The quantification of the main carbohydrates present in strawberry juices enriched with inulin and fructo-oligosaccharides (FOS) and preserved by non-thermal techniques (vanillin and ultrasound) was conducted, in addition to an investigation of the evolution of these compounds and their relationship with fungal deterioration over 14 days of refrigerated storage. A simple and environmentally friendly analytical approach based on high-performance liquid chromatography with a reflection index detector was developed for simultaneous determination of inulin, FOS and mono- and disaccharides present in the juices. When analyzing the evolution of carbohydrates during storage, a direct relationship between the consumption of sucrose and the growth of yeasts and molds (main spoilage flora in strawberry) was observed, especially in untreated samples (control). By contrast, no sucrose consumption was observed during storage of the treated sample, thus demonstrating the efficiency of the non-thermal treatments for controlling yeasts and mold growth. In turn, inulin and FOS added to juices were not degraded during storage. The results obtained in the present study demonstrate that non-thermal treatments are adequate for preventing the growth of deteriorative flora in strawberry juices and that the addition of inulin and FOS can be a good strategy for functionalizing them, as well as improving their nutritional properties. © 2017 Society of Chemical Industry.