The aim of this study was to evaluate the effect of a probiotic preparation consisting of two probiotic strains, Bacillus amyloliquefaciens CECT 5940 and Enterococcus faecium CECT 4515 (each 5 · 10(8) CFU/g feed), on faecal consistency, faecal microbiology and nutrient digestibility in adult healthy dogs. Sixteen beagles (eight males and eight females) were divided into two groups: the Control group (CON), which was fed the basal diet, and the probiotic group (PRO), which received the basal diet supplemented daily with 1 · 10(8) CFU for 39 consecutive days. Faecal score was assessed before (BS) and throughout the supplementation period (SP). Fresh faecal samples were collected before supplementation, before finishing the supplementation period and after 6 days of withdrawal for microbial enumeration and pH measurement. During the supplementation period, a digestibility trial was performed. There were no differences in faecal scores or the digestibility coefficients between groups. Between groups no statistical differences were found in most microbiota analysed or in faecal pH. However, during the supplementation period, pathogenic clostridia dropped significantly in Group PRO (5.64 vs. 2.94 ± 0.53 CFU/g faeces; p < 0.001), when compared with the period BS. The use of the probiotic preparation had no impact on nutrient digestibility by adult healthy dogs; however, it could stabilise faecal microbiota by decreasing pathogenic clostridia.