The aim of this study was to formulate novel snack rolls that are both prebiotic and gluten-free by incorporating value-added composite flours, including rice flour (RF), barley flour (BF), tiger nut flour (TF), and green banana flour (GBF), with the intention of enhancing the individuals with celiac disease. Physical properties, baking quality, sensory acceptability, and chemical properties were evaluated for the prebiotic formula (P) and prebiotic/gluten-free formula (P/GF). For the in vivo study, two different protocols were used: first protocol the rats were allocated into three distinct groups, each consisting of six rats: the normal control, group (1) fed on prebiotic formula, and group (2) fed on prebiotic/gluten-free formula. Second protocol concluded three groups of six rat pups, each selected for celiac disease induction, a normal control, a diseased group, and a treatment group fed on a prebiotic/gluten-free formula. Results proved that green bananas and tiger nut flours could have functional uses in the food industry and be applied as good ingredients for healthy food products. The biological findings revealed that both formulas improved the rats' health and can be effective in treating celiac disease. In conclusion, prebiotic and prebiotic/gluten-free formulas are considered safe and healthy for celiac disease patients.