Probiotics in the biofloc technology (BFT) system improve fish growth and immune response and promote a favorable intestinal microbiota balance. This study aimed to investigate the growth, hemato-biochemical parameters, bacterial resistance, and the number of intestinal bacteria colonies of Nile tilapia (6.23 g) reared in the BFT system with graded levels of Bacillus subtilis multiplicate (BSM) in the water. The multiplication of these microorganisms was performed in a biofactory. Fish were distributed into four different groups with graded BSM concentrations in the water of 0.00, 0.25, 0.50, and 0.75% (or 0; 750; 1500; and 2250 mL; called BSM0 (control), BSM25, BSM50, and BSM75, respectively). The experimental procedure had 45 days for growth performance evaluations and seven additional days of bacterial challenge with Aeromonas hydrophila. The experimental design was randomized into four treatments in triplicate (n = 20 fish per tank; initial stocking density of 0.50 kg m−3). Survival was 100% before and after the bacterial challenge. Increasing BSM in the BFT system had a positive linear effect on nitrite, nitrate, settled solids, hemoglobin, and hematimetric indices. BSM50 showed the highest specific growth rate, weight gain, intestinal total bacteria, and B. subtilis counts and the lowest feed conversion rate. In BSM50 and BSM75, liver glycogen levels and aspartate aminotransferase (AST) activity were higher and lower, respectively, than in the other treatments. Plasma total cholesterol, total proteins, albumin, and skin mucus total proteins and albumin were highest in BSM25. After the bacterial challenge, the number of lesions was lower in BSM75 than in the control group. In conclusion, we recommended BSM50 because it increased the growth performance and bacterial colonization in the intestine. It also decreased liver AST activity in Nile tilapia reared in the BFT system without compromising water quality and hematological and plasmatic parameters.