The present study evaluated the influence of different commercial agricultural by-products as a carbon source in a bifloc-based (BFT) culture system on growth performance, whole-body proximate composition, digestive enzyme activities, gut microbial abundance, and hepatopancreas histology of Pacific whiteleg shrimp, Litopenaeus vannamei post larvae (Pls). Three groups were designed, the first group was the control group, where the shrimp was reared in clear water (without carbon source addition and water exchange rate of 100\% two times a week) and fed with a commercial diet, in the second and third groups shrimp were reared in BFT systems using two different carbon sources, sugarcane bagasse (SB) and rice bran (RB) without additional feeding or water exchange. The initial stocking density was 16 Pls/liter with an average individual shrimp weight of 0.01 +/- 0.002 g and age (PL20). The experiment lasted 90 days. The water quality parameters were maintained at optimum levels during the experiment. The final body weight and specific growth rate of shrimp were significantly (p <= 0.01) higher in the control group than those reared in both SB and RB-based BFT. Meanwhile, the survival rate was significantly (p < 0.05) higher in BFT groups than in the control. The protease activity in shrimp stomach did not differ significantly. Meanwhile, protease, lipase, and amylase in the intestine showed a significant increase (p < 0.01) in BFT groups than those obtained in the control group. The total heterotrophic bacteria were significantly (p < 0.05) higher in BFT groups. Furthermore, the hepatopancreas histological status of shrimp reared in the SB-based BFT group showed an increase in the hepatopancreas tubules in the distal and B-cell zones (blister-like cells) by 16.83 and 34.89\%, respectively, compared to the control. This study revealed that BFT could be used as a natural feed without artificial diets, which influenced the gut microbiota of shrimp, increased digestive enzyme activities, as well as improved the histological structure of the hepatopancreas of shrimp. However, the success of this conditions under high stocking density still needs more investigation.