Yeast-based feed additives have emerged as promising functional feed additives (FFAs) to promote sustainable aquaculture development through enhanced gut health and immune modulation in fish. The present study evaluated the impact of autolysed brewer’s yeast (ABY) and soluble dried yeast extract (SDYE) in improving the intestinal and skin histology, immune response, and intestinal microbiome of Atlantic salmon parr (Salmo salar) over a 9-week feeding trial. Three experimental diets were produced: a control diet, a diet supplemented with ABY at 2.5 g/kg, and a diet supplemented with SDYE at 2.5 g/kg. These diets were administered to triplicate tanks of Atlantic salmon. The yeast-supplemented diets, especially ABY, improved intestinal mucosal fold length, lamina propria width, microvilli density, and intestinal goblet cell counts, as well as skin goblet cell counts. The yeast additives had no detrimental effects on the fish haematology, with no significant differences in haemoglobin concentration, red blood cell counts, and white blood cell counts among the treatment groups. Gene expression analysis revealed upregulation of il-1β and muc-2 in fish fed the ABY diet, indicating enhanced immune function and potentially mucosal protection. Intestinal microbiota analysis revealed Firmicutes as the most dominant phylum in all groups, followed by Actinobacteriota. Distinct bacterial community shifts were observed between the treatment groups, with a significant increase in the relative abundance of taxa such as Staphylococcus in yeast-supplemented diets and a significant decrease in Streptococcus and Weissella. Collectively, these findings suggest that the yeast additives, especially ABY, enhance gut health and immune function without compromising growth performance.