Most insoluble dietary fibers are known to be poorly fermented by the human gut microbiota. Since microwave (MW) treatment is used to enhance the susceptibility of insoluble materials to enzymatic hydrolysis in the food industry, we tested if MW would enhance insoluble dietary fibers (xylan, arabinan and arabinoxylan) fermentability in an in vitro gut fermentation model. As expected native xylan, arabinan and arabinoxylan were poorly fermented during 24 hours in vitro fecal fermentation. However, an increase in metabolites produced during their fermentation including the main SCFA (acetate, butyrate and propionate) could be observed for all tested dietary fibers after MW at distinct levels. Regarding physical changes, MW treatment increased xylan and decrease arabinoxylan solubility. Re-arrangements in tridimensional structure of dietary fibers were also observed by scanning electron microscopy after MW. Finally, DNA sequencing of resulting ferments indicate that MW treatment affected Bacteroides population as well as Clostrididiaceae, Lachnospiraceae, Ruminococcaceae and Enterobacteriaceae families if compared to native polymer ferments. Overall, MW treatment was effective in the promotion of a better gut fermentability of xylans, arabinans and arabinoxylans in vitro. Observed shifts in fiber solubility and tridimensional structure and their fermentation profile with stimuli of specific bacterial groups during in vitro fermentation of MW dietary fibers were dependent on their chemical structure. These results indicate that microwave treatment could be used as a strategy in the development of new prebiotic products.