T. macdonaldi is a carnivorous species endemic to the Gulf of California. Indiscriminate exploitation has put totoaba at risk, inducing the development of aquaculture procedures to grow it without affecting the wild population. However, aquafeeds increasing cost and low yields obtained with commercial feeds have motivated researchers to look for more nutritious and cheaper alternatives. Soybean (SB) is the most popular alternative to fishmeal (FM); however, antinutritional factors limit its use in carnivorous species. In this study, we analyzed B. subtilis 9b probiotic capacity to improve growth performance and health status of T. macdonaldi fed with formulations containing 30% and 60% substitution of fish meal with soy protein concentrate (SPC). In addition, we investigated its effect on internal organs condition, their capacity to modulate the intestinal microbiota, and to boost the immunological response of T. macdonaldi against V. harveyi infections. In this sense, we found that T. macdonaldi fed with SPC30Pro diet supplemented with B. subtilis 9b strain and 30% SPC produced better results than SPC30C control diet without B. subtilis and DCML commercial diet. Additionally, animals fed with SPC60Pro diet supplemented with B. subtilis 9b strain and 60% SPC doubled their weight and produced 20% more survival than SPC60C control diet without B. subtilis. Thus, B. subtilis 9b improved T. macdonaldi growth performance, health status, modulated intestinal microbiota, and increased animal’s resistance to V. harveyi infections, placing this bacterium as an excellent candidate to produce functional feeds with high levels of SPC.