Bioflocs are composed of a complex microbial community formed not only by bacteria but also by algae, fungi, protozoa, rotifers, and other organisms. The bacterial communities of the gastrointestinal tract may naturally differ among different culture systems. The objectives of this study were to analyze the stomach contents of Litopenaeus vannamei shrimp cultivated in biofloc systems with different inoculation percentages and to describe which organisms and biomolecules are found in the shrimp under these conditions, thus determining the optimal culture system based on the microbial content. The experiment was conducted at the Marine Aquaculture Station (EMA) of the Oceanographic Institute of the Federal University of Rio Grande and was designed with four treatments and four replicates: (I) clear water (CW); (II) 25% biofloc inoculum (BF 25%); (III) 50% biofloc inoculum (BF 50%); and (IV) 100% biofloc inoculum (BFT 100). In all cases, mature biofloc inocula from previous cultures were used. The zootechnical performance of the shrimp was monitored weekly through biometric assessments, and the physical and chemical parameters of the water (temperature, dissolved oxygen, pH, ammonia, and nitrite) were measured daily. The abundance of the microbial community primarily influences water quality across treatments and may explain the different effects observed under varying conditions. Treatments with bioflocs achieved higher survival rates than the clear water treatment. The microorganisms identified in the stomachs of shrimp cultivated in biofloc systems included oocysts, ciliates, flagellates, diatoms, free-living coccoids, free and attached filamentous organisms, bacilli, and vibrios, with the stomach microbiota being determined by the culture environment. Therefore, according to the results obtained in the experiment, the reuse of bioflocs at 25% of the total volume is effective in maintaining water quality and in colonizing the shrimp's microbiota.