A comparison of the growth performance of Penaeus vannamei was ascertained by supplementing the potential probiotics isolated from a biofloc system incorporated through feed. Post-larvae shrimp (0.045 ± 0.005 g) were stocked at a density of 500/m3 in FRP tanks (500 L) in triplicates for a period of 60 days. A total of 40 bacterial strains were isolated from previous biofloc culture trials and tested for their antimicrobial activity against the pathogen Vibrio parahaemolyticus. Among these, Bacillus megaterium, Exiguobacterium profundum, Pseudomonas balearica, and Pseudomonas stutzeri showed higher antimicrobial activity. The treatment groups included clear water with no probiotics (CW), clear water + isolated probiotic (CW + IP), biofloc alone (BFT), and biofloc + isolated probiotic (BFT + IP), in triplicates. Distillery spent wash was used as a carbon source for biofloc development and maintenance. A probiotic concentration of 1 × 109 cfu/g was supplemented throughout the trial. The recorded water quality parameters (pH, alkalinity, calcium, and magnesium) were observed to be significant among the experimental groups (p ≤ 0.05). The highest weight gain (2.43 g), SGR, PER, and lower FCR values were recorded in BFT + IP. The lowest values of total Vibrio were found in BFT. The histology analysis revealed that there was a mild increase in the B and R cell vacuoles in the hepatopancreas of CW and BFT + IP, whereas mild degeneration was found in the intestine of CW and CW + IP. Microbiome analysis of the shrimp gut revealed that Proteobacteria was the most abundant phylum in all experimental groups. P. balearica, K. pneumoniae, P. stutzeri, and E. profundum were present in the gut of C, whereas P. balearica, K. pneumonia, and P. stutzeri were present in the gut of CW + IP and BFT + IP. The results proved that the probiotics isolated from biofloc colonized in shrimp gut could play a promising role in aquaculture.