This study aimed to evaluate the effects of a probiotic mix composed of Bacillus spp. and benzoic acid, all together and separately, in intestinal microbiology, liver, and intestinal histology, as well as in the composition of the intestinal microbiota by high-throughput sequencing analysis of juvenile Nile tilapias Oreochromis niloticus. Three hundred and twenty fish were divided into four experimental groups with four replicates. They were fed for 54 days: control (no supplementation), 0.1% benzoic acid (BA0.1%), mix of Bacillus spp. (Bacillus), and feed supplemented with Bacillus spp. and 0.1% benzoic acid (B+BA0.1%). Classical microbiological analysis showed that B+BA0.1% increased the concentration of total heterotrophic bacteria (4.94 ± 0.77) compared to the control group (4.43 ± 0.90). The results showed significant liver changes such as ballooning, congestion of large vessels, and pancreatic congestion between treatments B+BA0.1% and BA0.1%, the latter resulting in less (15.91 ± 16.61) pancreatic congestion than the other treatments. Vacuolation in the intestine was greater in supplemented animals with BA0.1%, B+BA0.1%, and Bacillus spp. than in the control group. The width of the villi was greater in the group supplemented with B+BA0.1% (22.19 ± 10.91) than in the Bacillus group. The abundance of Firmicutes and Bacteroidetes was higher in the B+BA0.1% group. Cetobacterium somerae was more abundant in the Bacillus and B+BA0.1% groups in the diversity index. Notably, joint supplementation with the probiotic mixture Bacillus spp. and 0.1% benzoic acid had a synergistic effect on the intestines of tilapia, positively modulating the intestinal microbiota.