The study assessed the influence of rapeseed meal (RSM) fermented using Bacillus subtilis 87Y on the feed microbiota, intestinal microbiota, blood biochemical parameters, and content of minerals in the blood plasma and faeces of piglets. Modulation of the microbial composition of feed containing fermented rapeseed meal (FRSM) and of the faeces of pigs consuming it was observed. There was a significant increase in the number of lactic acid bacteria (LAB) and a decrease in the total number of coliforms and Clostridium perfringens in the faeces of animals from the experimental groups. FRSM in the diet of piglets was shown to improve the mineral balance by increasing the levels of P, Ca, and Mg in the blood plasma and reducing their amount in the faeces. A beneficial effect on parameters of protein and lipid metabolism was also noted, resulting in an increase in the levels of total protein (TP) and albumins (ALB) and a reduction in triacylglycerols (TG) and low-density lipoprotein (LDL) cholesterol in the blood plasma of the piglets. The research results indicate that the presence of FRSM in the diet of weaners can be a preventive factor in intestinal dysbiosis and support the maintenance of homeostasis