The reliance on fishmeal as a primary feed source in aquaculture lessens the potential for the industry to provide an environmentally sustainable alternative to wild-caught fisheries. Our study used replicate recirculating, closed-containment salmon farms to compare the microbial communities of farms using alternative fishmeal-free diets to those traditional diets. We sampled both fish tissue (intestine and gills), and the farm environment (biofilters and water).