The present study tested the symbiotic effects of dietary multi-strain Bacillus probiotics (MSB) (Bacillus licheniformis, B. pumilus, and B. subtilis) in Nile tilapia (Oreochromis niloticus) exposed to Aspergillus flavus infection. Furthermore, this study investigated water quality, growth performance, blood metabolites, histological morphology, immune regulatory genes, and resistance to A. flavus infection. For 70 days, fish (n = 240) were divided into four groups in triplicate: T0 (control group; MSB0), T1 (1 g/kg, MSB1), T2 (2 g/kg, MSB2), and T3 (3 g/kg, MSB3). The immune response was then assessed by challenging all fish groups with the A. flavus pathogen. The results showed that the rearing water quality, fish growth, and blood parameters, as well as total proteins, albumin, globulins, and amylase activity were significantly (P < 0.05) increased in all MSB-treated groups with the best results in MSB2 and MSB3 groups. Meanwhile, the activities of aspartate aminotransferase (AST), alanine aminotransferase (ALT), cholesterol, and glucose levels were significantly (P < 0.05) modulated, particularly at higher concentrations of the probiotic mixture (MSB3 group). Fish fed with various levels of MSB showed a maintained histological structure of the hepatopancreas, intestine, and spleen tissues. The mRNA expression of growth hormone (GH), insulin-like growth factor-1 (IGF-1), insulin-like growth factor receptor-1 (IGF-1R), and interleukin-8 (IL-8) were increased in a dose-dependent manner due to MSB dietary inclusion (P < 0.05). Conversely, the mRNA expression of interleukin-1β (IL-1β) gene was significantly decreased in MSB groups compared to untreated group (P < 0.05). Surprisingly, supplemented groups in Bacillus spp. probiotics exhibited significant modulations in all computed parameters. MSB supplementation improved the pathogenic tolerance of tilapia after change with A. flavus. The integration of growth performance, biochemical, and transcriptomic results confirms that the dietary intervention of multi-strain Bacillus spp. is symbiotic and enhances the benefits for the maintenance of O. niloticus’ health, growth, and digestion. This is achieved by supporting growth genes, reducing inflammatory genes, and enhancing immune-antioxidant resistance to combat A. flavus infection.