The aim of the study was to determine how effective microorganisms influence meat quality, the microstructure of the longissimus lumborum muscle, and electrophoretic protein separation. The study group consisted of 150 piglets divided into three feeding groups: C, E1, and E2. The feeding groups included C—a standard fodder blend with a full share of post-extracted soya meal; E1—a 50%/50% mix of pea and lupine/soya bean in phase I of fattening and a 75%/25% mix of pea and lupine/soya bean in phase II of fattening; and E2—a 50%/50% mix of pea and lupine/soya bean in phase I of fattening and in 100% pea and lupine in phase II of fattening. The experimental factor was the addition of the EM Carbon Bokashi probiotic to the diet (C + EM, E1 + EM, E2 + EM). Influence of the feeding system on the following parameters was also estimated. After slaughter, the meat quality, LL muscle microstructure, and electrophoretic protein separation were assessed. In the C + EM group, a lower water-holding capacity was demonstrated. Meat from pigs fed the effective microorganism additive was much harder in the E1+EM group compared to meat from pigs from the E1 group. A beneficial effect of effective microorganism was found in the E2 + EM group, where less thermal leakage from the meat was demonstrated. A beneficial effect of the feeding system on thermal leakage and loin eye area in the E2 + EM group was demonstrated. In the C + EM group, a lower total number of muscle fibers was demonstrated. The addition of effective microorganism caused an increase in the diameter of fast twitch fibers in the E1 + EM group. In the same group of pigs, effective microorganisms caused a lower proportion of fiber fission. This nutritional variant appears to be the most appropriate for proteins as well, because it led to the most favorable percentage of individual proteins after effective microorganisms supplementation in the longissimus lumborum muscle.