Arabinoxylans (AX) consumption has been related to the treatment and prevention of cardiovascular diseases, type II diabetes, colorectal cancer and obesity. The beneficial health effects are conferred through gut microbiota modulation, and therefore, they have been proposed as potential slowly fermentable prebiotic candidates. As the mechanisms are not yet well understood, the prebiotic potential of AX from brewer's spent grain (BSG) has been investigated. Two types of AX from BSG (AX1 and AX2) of different length and branching averages were fermented with human faecal inocula and compared to fermented cultures containing a commercial prebiotic (fructooligosaccharide (FOS)) and cultures with no added carbohydrate (control). Results demonstrated that the AX were extensively metabolised after 48 h of fermentation. The pH decreased along fermentation and the lowest value was achieved in AX1 cultures. The production of short chain fatty acids (SCFA) was higher in AX cultures than in cultures containing FOS and controls, with AX1 presenting the highest concentrations. The stimulatory effect of beneficial bacteria was higher in AX cultures, and AX2 presented the highest positive effect. Prebiotic potential of AX from BSG was confirmed by the production of SCFA and the modulation of gut microbiota, especially by the high increase in bifidobacteria populations.