The aim of this study was to evaluate the role of the intestinal microbiota in soybean meal enteritis. Three groups of Atlantic salmon (Salmo salar) were fed for 35 days with different diets: a control diet (CD) containing 510 g kg−1 fishmeal, diet 1 (D1) containing 378 g kg−1 of soybean meal and diet 2 (D2) containing D1 supplemented with two viable lactic acid bacteria (LAB). As expected, the fish fed with D1 showed clear signs of distal intestinal inflammation during the study compared with the fish fed CD. For the fish fed with D2, the addition of LAB diminished the inflammation at day 28, but did not abolish it. Microbiological analysis demonstrated that specific bacterial groups were not correlated with the development of enteritis, but were correlated with the three diets. Microbacterium, Pseudomonas, Lactococcus lactis sp. cremoris and Aeromonas VIa were correlated with the CD, Aeromonas VIb and Sporosarcina aquimarina were correlated with D1, and Alcaligenes, Acinetobacter, L. lactis sp. lactis and Carnobacterium maltaromaticum were correlated with D2. Shewanella was not affected by the diet and was present in all fish intestines. Our study suggests that LAB may modulate intestinal inflammation; however, the role of the microbiota in the aetiology of enteritis in fish still requires further study.