The dietary fiber gap that is present in many countries co-exists with a low intake of grain legumes (pulses) that have 2–3 times more dietary fiber than cereal grains that are commonly recommended to increase fiber intake. Given the relationships among dietary fiber, gut health and chronic disease risk, a study was undertaken in a preclinical mouse model for obesity to examine how commonly consumed pulses, i.e., chickpea, common bean, dry pea and lentil, would impact gut microbes, intestinal function, and adiposity. Pulses were fed to C57BL/6 mice at similar levels of protein and fiber. Bacterial count in the cecum was elevated 3-fold by pulse consumption. At the phylum level, a 2.2- to 5-fold increase in Bacteriodetes relative to Firmicutes was observed. For Akkermansia muciniphila, a health-beneficial bacterium, differential effects were detected among pulses ranging from no effect to a 49-fold increase. Significant differences among pulses in biomarkers of intestinal function were not observed. Pulses reduced accumulation of lipid in adipose tissue with a greater reduction in the subcutaneous versus visceral depots. Metabolomics analysis indicated that 108 metabolites were highly different among pulse types, and several compounds are hypothesized to influence the microbiome. These results support recent recommendations to increase consumption of pulse-based foods for improved health, although all pulses were not equal in their effects.