The aim of this study was to: (1) provide controlled fermentation of narrow-leafed lupine seeds; (2) monitor seed composition, and (3) determine the influence of fermentation on the performance, gut environment and physiology, and selected blood metabolic parameters, in young pigs. Firstly, the effect of 24 h lupine seed fermentation by bacteria and yeast on seed chemical composition was determined. It increased contents of crude protein, crude fiber and ash, but reduced nitrogen-free extractive levels. The amino acid profile of fermented lupine (FL) was similar to that of raw lupine (RL) seeds, whereas the contents of oligosaccharides and P-phytate decreased significantly, in contrast to alkaloids. In fermented feed, pH dropped from 5.5 to 3.9. In the 28-day experiment, 24 male pigs were divided into three groups. The control group was fed a soybean meal diet (SBM), whereas in the experimental diets, 50% of SBM protein was replaced by RL or FL. Afterwards, eight pigs from each group were euthanized and their digesta and blood samples were collected. The FL use did not affect pigs’ performance, nor their metabolic, microbial and most gastrointestinal tract parameters, but influenced crypt depth. Fermentation affected concentrations of short chain fatty acids and p-cresole in the proximal colon segment. In the small intestine, the levels of acetate and butyrate decreased, and, in the caecum, the propionate level decreased. Fermentation significantly lowered the pH of the middle colon digesta and ammonia contents compared to RL. A part of SBM may be successfully replaced by RL and FL in young pigs’ diets.