Duplicate groups of Atlantic salmon (Salmo salar), kept in saltwater, were fed fish meal based cold-pelleted diets where graded levels of native or extruded non-starch polysaccharides (NSP) from soybeans replaced cellulose, at a total NSP level of 100 g kg−1 for 28 days. The study also included a diet where defatted soybean meal (SBM) constituted the NSP at a level of 100 g kg−1 and a reference diet without NSP supplementation.The SBM diet resulted in a significant reduction in faecal dry matter content, apparent digestibilities of starch and organic material, and growth, and an increased faecal output of several elements (K, Na, Zn), compared to all the other diets. Morphological changes were only seen in the intestine of the fish fed the SBM, i.e. the diets holding purified soy-NSP did not induce enteritis. When compared to the diet without NSP, cellulose addition increased faecal dry matter, while inclusion of native soy-NSP reduced it. Dry matter in faeces and apparent digestibility of crude protein decreased in a linear manner, while the digestibility of starch and faecal output of K and Na increased linearly when native soy-NSP replaced graded levels of cellulose from 0 to 100 g kg−1 feed. When diets with 75 or 100 g kg−1 of native NSP and extruded soy-NSP were compared, fish fed native soy-NSP had reduced faecal dry matter, higher digestibility of starch, and increased faecal output of Cu, Fe, and K. Dry matter in faeces and faecal output of Cu was lower for the highest inclusion level, while digestibility of starch and faecal output of Mn and K were higher.In conclusion, soy-NSP was inert compared to the fish meal reference, with respect to nutrient digestibilities and intestinal pathologies, but affected faecal mineral excretion in Atlantic salmon.