Prebiotics alter microbial communities by supplying carbon to specific bacteria that benefit the host. However, the effect of prebiotics added to the culture water on shrimp production and bacterial composition has not been demonstrated. Therefore, this study evaluated the effects of four prebiotics — short-chain fructooligosaccharide, galactooligosaccharide, inulin, and mannan-oligosaccharide — and two non-prebiotic carbohydrates — sucrose and wheat starch — on shrimp growth, nutrient composition of shrimp muscle and biofloc, biofloc concentration, and bacterial profiles in biofloc and gills, hepatopancreas, and intestine of Penaeus vannamei. Shrimp (6.0 ± 0.5 g) were stocked into 36 tanks (72 shrimp/m2) and raised in a biofloc technology system consisting of two phases: an autotrophic-dominated phase (days 0–4) and a heterotrophic-dominated phase (days 5–26). The prebiotic and non-prebiotic carbohydrates were added to the water at a rate of 3 % of the feed provided. Key findings revealed that adding prebiotics to the water did not affect shrimp growth. Notably, shrimp muscle from the mannan-oligosaccharide treatment exhibited a significantly higher lipid content than that from the galactooligosaccharide treatment (p ≤ 0.05). No significant effect was observed on the nutrient composition of biofloc. Biofloc concentration was lower in the wheat starch treatment (p ≤ 0.05). Finally, the prebiotics altered the bacterial composition of biofloc and shrimp gills, hepatopancreas, and intestine. These results revealed that adding prebiotics to the culture water of a biofloc system has an effect on shrimp quality and microbial communities of biofloc and various shrimp tissues, suggesting their potential benefit on shrimp production and health.