Sustainable aquaculture practices can help meet the increasing human demand for seafood, while easing pressures on natural fish populations. Studies aimed at increasing fish production in aquaculture have included supplementary dietary probiotics that often promote general health and enhanced growth rates by altering the microbiome of the host. Steelhead trout (Oncorhynchus mykiss) is anadromous, like salmon, and it is a subspecies of rainbow trout capable of rapid growth, making it an attractive fish to the aquaculture industry. In this study, the impact of feeding a Bacillus subtilis probiotic on the bacterial microbiome of steelhead trout was examined temporally across several stages of animal development, from eggs (day -19) through 184 days after hatching, in relation to physiological measures. Diets included: commercial feed only as a control (A), continually-fed probiotic top-coated on commercial feed (B), commercial then switch to probiotic feed (C), or probiotic then switch to commercial feed (D). Validation of probiotic concentrations on feed and in fish tissues was performed using CFU/g and qPCR, respectively. Fish growth was measured and samples for intestinal microbiome analyses were collected at multiple timepoints during fish development. Fish fed diet D yielded higher weights than the other three diets, with little impact on other biometric parameters. However, bacterial microbiome analysis indicated an increasing trend of overall alpha diversity from the egg stage to day 29 for fish fed the various diets with diet D having the highest diversity. Fish fed diets A and D maintained a high alpha diversity beyond day 29 in contrast to a decreased trend for fish still being fed probiotics in diets B and C. The fish fed diets B and C harbored a significantly higher relative abundance of Bacillus sp. in their total microbiomes (feces + mucosa). Interestingly, the mucosal-only microbiome indicated little variation between the four groups of fish. Feeding the probiotic earlier in development, during the hatchery phase, to influence bacterial microbiome composition in the intestine (rather than later after the microbiome has been established) appears to be a more effective aquaculture practice by enhancing microbiome diversity while enabling higher fish yields.