Abstract Macronutrient and micronutrient deficiencies in the fish diet can affect fish growth rate, ability to resist disease, and fillet quality. Determination of effective dose of developed feed additives consisting of chelate compounds of biogenic elements and probiotic preparation based on Bacillus subtilis. Young rainbow trout were divided into four groups consisting of 100 fish each. The control group received standard food; the experimental groups received food with chelates and probiotics in different concentrations. At the end of the experiment (30 days), the middle intestine histology and morphometric parameters were studied. The use of chelated compounds alone affected the state of the intestinal villi and the infiltration of the epithelium by lymphocytes. The addition of a probiotic had a positive effect on the migration of immune cells in the intestinal villi; however, the probiotic in high concentrations contributed to a decrease in the number and area of goblet cells. Synergistic effects of chelated compounds and probiotic preparations on the morphometric parameters of the medium intestine were observed. In the proper doses, the studied feed additives might be recommended for rainbow trout farming under industrial aquaculture conditions.