The aim of this work was to study the effect of protein source / availability on the intestinal microbiota, digestive traits and nutritional performance of early-weaned rabbits. The effects of supplemental antibiotics in the drinking water were also evaluated. Four isoenergetic and isofibrous diets were formulated: a control diet with a high protein (207 g/kg dry matter (DM)) and lucerne hay content (HPHL), a diet with low crude protein (CP) (179 g/kg DM) and high lucerne hay content (LPHL) and low protein diets in which the lucerne hay in diet LPHL was replaced partially (LPML) or totally (LPLL) with soya-bean protein concentrate. Rabbits, weaned at 25 days (52 per diet), were fed the experimental diets for a 2-week period and thereafter received a commercial diet until 56 days of age. The incidence of mortality was investigated using 70 animals per diet without supplemental medication. The profile of the ileal microbiota was studied at 35 days of age in rabbits treated (18 per diet) or not (12 per diet) with antibiotic. As expected, supplementation with antibiotics effectively reduced fattening mortality rate and microbial biodiversity. However, lowering of also the dietary CP content led to a reduction in the mortality rate ( P < 0.05), both in animals treated with (by 80%) or without (by 39%) antibiotics. In addition, there was a reduction ( P < 0.05) in the frequency of Clostridium perfringens in non-medicated animals. Neither jejunal morphology nor growth performance, over the whole fattening period, was affected by dietary CP content of the experimental diets. However, with HPHL, feed efficiency was higher (by 4.8%; P < 0.01) than with LPHL diets. Substitution of lucerne hay with soya-bean meal in low protein diets did not affect apparent faecal or ileal digestibility of DM and CP. However, the ileal digestibility of cystine, alanine, aspartic acid, and proline was lowered ( P < 0.05) with increasing substitution by soya bean. Nevertheless, ileal CP flow, incidence of mortality and presence of C. perfringens were unaffected. Our results suggest that a reduction in dietary CP, resulting in reduced lumenal flows of nitrogen through the ileum, may be beneficial for young rabbits and limit the numbers of potentially harmful bacteria in the lower gut. Modulation of dietary CP should be contemplated as a strategy to increase the intestinal health in rabbits.