The study’s objective was to ascertain whether a nutritional multivitamin and mineral supplement enriched with two different dietary fibers influences microbiota composition, mineral absorption, and some immune and metabolic biomarkers in adult rats. Nine-week-old Wistar rats were randomly assigned into four groups: the reference group; the group receiving a daily supplement based on a food matrix with proteins, vitamins, and minerals; and two other groups receiving this supplement enriched with inulin (V + I) or acacia (V + A) fiber for four weeks. Microbiota composition was determined in cecal content and mineral content in fecal, blood, and femur samples. Intestinal IgA concentration, hematological, and biochemical variables were evaluated. Both V + I and V + A supplementations increased Firmicutes and Actinobacteria phyla, which were associated with a higher presence of Lactobacillus and Bifidobacterium spp. V + A supplementation increased calcium, magnesium, phosphorus, and zinc concentrations in femur. V + I supplementation increased the fecal IgA content and reduced plasma total cholesterol and uric acid concentration. Both fiber-enriched supplements tested herein seem to be beneficial to gut-health, although differently.