The objectives of the present study were to investigate the effects of inulin and fructooligosaccharides (FOS) on growth performance, whole body and fillet chemical composition and intestinal microbiota of rainbow trouts reared under fish farming conditions. Trouts fed inulin- or FOS-containing diets (5 and 10 g kg−1) exhibited significant (P = 0.030) body weight gain improvements compared with controls. An increase in gross energy (P = 0.044) and Ca content (P = 0.034) in the whole body of trouts was observed for prebiotic treatments. A decrease in crude protein content (P = 0.009) and a tendency to increase total lipid and gross energy contents (P = 0.090 and P = 0.069, respectively) were detected in the fillet tissue for prebiotic treatments. These results clearly indicate that inulin and FOS improved the intestinal absorption of Ca and that the increased amount was predominantly incorporated into bone tissue. Inulin reduced (P = 0.027) the intestinal population of Vibrio spp. in the distal region to such an extent that no viable counts were detected. The presence of Flavobacterium spp. was not detected in any group, and the numbers of Aeromonas spp., Pseudomonas spp. and Gram-positive bacteria were not affected (P > 0.05).