The present research explored the effects of Bacillus subtilis on water quality, growth, immune responses, endotoxemia and protection against lipopolysaccharide (LPS) damages in Nile tilapia Oreochromis niloticus under biofloc system. B. subtilis was added at 0, 1, 2, 3 and 4 grams (1.19 × 108 CFU/g) per kg of basal diet, named T1 (control), T2, T3, T4 and T5, respectively, and fed to fish (14.82 ± 0.42 g) for 50 days. The concentrations of TAN, NO2 and NO3 were significantly reduced, and fish fed probiotics displayed significantly better growth performances versus the control, concomitantly with significantly enhanced activities of digestive enzymes. They also showed significantly declined serum glucose and cholesterol vice versa significantly improved immune responses (total protein, albumin, globulin, lysozyme, alternative complement, protease, immunoglobulins, alkaline phosphatase and respiratory burst), antioxidant capacity (superoxide dismutase, total antioxidant capacity, malondialdehyde) and skin mucus parameters (total protein, lysozyme, alternative complement, protease, immunoglobulins). Meanwhile, significantly lower endotoxin (LPS) concentrations were detected in the intestines and serum of fish fed probiotics. LPS challenge induced profound oxidative stress and impaired immune responses. Interestingly, probiotic alleviated LPS‐induced damages and restored mentioned parameters. In conclusion, B. subtilis effectively enhanced fish production, immunity and protection against LPS‐induced damages in tilapia under biofloc system.