Chinook salmon is a native species of the Canadian Pacific coast with potential economic and environmental benefits for aquaculture. However, its production is jeopardized by low tolerance to high densities and disease susceptibility. Due to this, Chinook salmon represents a great candidate for evaluating the effect of non-polluting alternatives to vaccines and antibiotics, such as probiotics. Preliminary studies have suggested that certain probiotic strains may be able to enhance fish growth, antioxidant activity, food digestibility, modulate the host microbial community in the digestive tract, and prevent bacterial infections. However, there is currently no evidence of its effects in Chinook salmon. Here, we used the commercially available, low-cost multi-strain probiotic used by humans, to determine the impact on Chinook salmon growth, survival, immune response, and gut barrier integrity. Fish were randomly assigned to four netpens and given either regular (control) feed or supplemented with probiotics for 4, 10, or 14 months. After this, fish were transferred to troughs and challenged with Vibrio anguillarum. Probiotic supplementation for 14 months decreased mortality by ∼10% compared to the control treatment. However, no positive effects of this probiotic supplementation on fish growth occurred. Despite the improvement in survival associated to long-term probiotic supplementation, the expression of the immune genes il1b, il8, il10, tnfa, camp, hamp, and transferrin in head kidney, spleen, and hindgut tissues did not fully provide the specific innate immune mechanisms that could be associated with a better protection. Decreased expression of cldn1 and ocln in fish supplemented for 14 months compared to 4- and 10-months suggested that probiotic treatment during the freshwater and saltwater cycle confers a better protection and intestinal integrity, resulting in an improved survival. Although it was not possible to observe differences in IgM and IgT protein levels between probiotic-supplemented fish and the control treatment in plasma, head kidney, spleen, and hindgut, this study represents the first measurement of total IgT protein levels in Chinook salmon. In summary, probiotic supplementation modulated the early inflammatory response against V. anguillarum infection and helped improve the survival of Chinook salmon aquaculture in an environmentally sustainable manner when applied in freshwater and up to the transition to saltwater growth phase.