The aim of the study was to determine the influence of the effective microorganisms (EM) on performance parameters, intestinal morphology and gene expression in the jejunal mucosa in pigs under different feeding regimes. The study group comprised of 150 piglets divided into three feeding groups: C, E1 and E2. Feeding groups included: C—standard fodder, blend with a full share of post‐extracted soy meal, E1—in the phase I of fattening: pea and lupin/soybean 50/50%; in the phase II of fattening: pea and lupin/soybean 75/25%, and E2—in the phase I of fattening: pea and lupin/soybean 50/50%; in the phase II of fattening: pea and lupin 100%. The experimental factor was addition of a probiotic EM Carbon Bokashi to the diets (C + EM, E1 + EM and E2 + EM). After slaughter, histological evaluation and gene expression analysis were performed. The highest intestinal villi were reported in E2 + EM. A higher intestinal absorption area was demonstrated in groups C + EM and E2 + EM. An interaction between feeding and EM Bokashi supplementation was found in villus surface area crypt depth, villus height/crypt depth and number of goblet cells. Mucosa thickness and number of goblet cells was the largest in E2 + EM. Gene expression of FABP4 increased in E1, and GLUT2 decreased in E2. Gene expression of IL10 and FABP4 increased in E2 + EM. The results indicate that the E2 diet is more optimal for EM Bokashi supplementation, because in this group, EM positively influenced the morphological characteristics of the porcine jejunum and caused an increase in the expression of genes related to the metabolism and functioning of the gastrointestinal tract.