A 2 × 2 factorial experiment was performed to investigate the interaction between a high- and low-crude-protein (CP) diet (200 v. 140 g/kg) and inulin supplementation (0 v. 12.5 g/kg) on nutrient digestibility, nitrogen (N) excretion, intestinal microflora, volatile fatty acid (VFA) concentration and manure ammonia emissions from 24 boars (n = 6, 74.0 kg live weight). The diets were formulated to contain similar concentrations of digestible energy and lysine. Pigs offered the high-CP diets had a higher excretion of urinary N (P < 0.001), faecal N (P < 0.01) and total N (P < 0.001) than the pigs offered the low-CP diets. Inulin supplementation increased faecal N excretion (P < 0.05) and decreased the urine N : faeces N ratio (P < 0.05) compared with the inulin-free diets. There was no effect (P > 0.05) of dietary treatment on N retention. There was an interaction (P < 0.05) between dietary CP concentration and inulin supplementation on caecal Enterobacteria spp. Pigs offered the diet containing 200 g/kg of CP plus inulin decreased the population of Enterobacteria spp. compared to those with the inulin-supplemented 140 g/kg CP diet. However, CP level had no significant effect on the population of Enterobacteria spp. in the unsupplemented diets. Inulin supplementation increased caecal Bifidobacteria (P < 0.01) compared with the inulin-free diets. There was no effect of inulin supplementation on VFA concentration or intestinal pH (P > 0.05). Pigs offered the 200 g/kg CP diets had higher (P < 0.05) manure ammonia emissions from 0 to 240 h of storage than pigs offered the 140 g/kg CP. In conclusion, inulin supplementation resulted in an increase in Bifidobacteria concentration and a reduction in Enterobacteria spp. at the high CP level indicating that inulin has the ability to beneficially manipulate gut microflora in a proteolytic environment.