Simple SummaryThe fermented feed component in pigs‘ diet may influence the microbiota of the gastrointestinal tract, improve the use of nutrients from the diet, and reduce the level of excreted N and P. The aim of this study was to investigate the effects of raw and Candida utilis-fermented yellow and narrow-leaved lupine seeds on the apparent ileal digestibility coefficients of protein and amino acids and the metabolic activity of the intestinal microflora in five cannulated male pigs. Fermentation significantly improved the ileal digestibility of protein, asparagine, threonine, tyrosine, histidine, and arginine in the lupine seeds and increased the counts of total bacteria and yeast, the pH value, isobutyrate and isovalerate concentrations in the ileal digesta, but decreased the dry matter and ammonia content. The narrow-leaved lupine seeds were characterized by higher digestibility of asparagine, threonine, serine, alanine, valine, isoleucine, and arginine. The digesta of the pigs fed with these seeds had higher counts of lactic acid bacteria and moulds but lower total bacteria count than the digesta of the pigs fed with yellow lupine seeds.The aim of this study was to investigate the effects of raw and Candida utilis-fermented yellow (YL) and narrow-leaved lupine (NL) seeds on the apparent ileal digestibility coefficients (AID) of protein and amino acids in pigs and the metabolic activity of their intestinal microflora. Five cross-bred castrated 25-kg barrows were surgically fitted with a T-cannula in the distal ileum and housed individually in metabolic cages. They were fed five semi-synthetic diets containing only one source of protein: soybean meal (SBM), raw or fermented yellow lupine seeds (RYL or FYL), raw or fermented narrow-leaved lupine seeds (RNL or FNL). The study period consisted of six-day adaptation to the diet and one-day collection of digesta, which was sampled for microbial and chemical analyses. The AID coefficients of protein and amino acids were calculated with the marker method with TiO2. One-way (feed effect) and two-way (variety effect, fermentation effect) analysis of variance (ANOVA) with Duncan’s test at p < 0.05 were applied. The digesta from the SBM and FNL variants had significantly higher (p < 0.05) AID coefficients of protein, asparagine, threonine, serine, isoleucine, leucine, histidine, and tyrosine, whereas the SBM variant was characterized by the lowest AID of cystine and the highest AID of alanine and methionine (p < 0.05). The ileal digesta of the pigs fed with FYL contained more bacteria, whereas the count of yeast was higher in the FNL variant. The digesta of the pigs from the FNL and RYL variants had the highest count of moulds (p < 0.05), whereas the digesta in the FYL, SBM, and RNL variants had almost no moulds at all. The ileal dry matter content was significantly lower in SBM group. The lowest pH was noted in the RYL variant (p < 0.05). The content of ammonia and total volatile fatty acids in the ileal digesta of the SBM variant was the lowest (p < 0.05). Fermentation significantly improved the AID of protein, asparagine, threonine, tyrosine, histidine, and arginine, increased the counts of total bacteria and yeast, the pH value, and isobutyrate and isovalerate concentrations, but decreased the dry matter and ammonia content (p < 0.05). The digesta of the NL variants was characterized by higher AID of asparagine, threonine, serine, alanine, valine, isoleucine, and arginine, and higher counts of LAB and moulds but lower total bacteria count than in the YL variants. The ileal pH was lower in the YL variants, where higher isobutyrate and butyrate concentrations (p < 0.05) were observed. To sum up, fermentation increased the counts of the ileal microbiota and improved the digestibility coefficients of protein and some amino acids. The narrow-leaved lupine seeds resulted in more positive changes in the digesta of growing pigs than yellow lupine.