Background This study investigated the effects of different non-starch polysaccharide (NSP) sources with NSP degrading enzymes (NSPases) and the influence on the mucosa-associated microbiota and intestinal immunity of nursery pigs, on growth performance and carcass traits at market weight. Methods One hundred and sixty newly weaned pigs at 7.0 +/- 0.3 kg body weight (BW) were allotted in a 2 x 2 factorial with NSP sources and NSPases serving as factors. The 4 dietary treatments were: DDGS, corn distillers' dried grains with solubles as source of NSP; DDGS + NSPases (DDGS +), DDGS with xylanase at 0.01%, 3,000 U/kg of feed and beta-mannanase at 0.05%, 400 U/kg of feed; SHWB, soybean hulls and wheat bran replacing corn DDGS as the source of NSP; SHWB with NSPases (SHWB +), SHWB with xylanase at 0.01%, 3,000 U/kg of feed and beta-mannanase at 0.05%, 400 U/kg of feed. Pigs were fed for 37 d and housed in groups of 4 pigs per pen. At d 37, the median body weight pig in each pen was euthanized for sampling to analyze intestinal health parameters. Remaining pigs were fed a common diet for subsequent phases to evaluate the carryover effect on growth and carcass traits. Results The SHWB decreased (P < 0.05) the relative abundance of Helicobacter, tended to increase (P = 0.074) the relative abundance of Lactobacillus, increased (P < 0.05) immunoglobulin G (IgG) in the jejunal mucosa, tended to increase (P = 0.096) the villus height (VH) in the jejunum, and tended to improve ADG (P = 0.099) and feed efficiency (P = 0.068) during phase 1 compared to DDGS treatment. Supplementation of NSPases increased (P < 0.05) Shannon index of diversity, increased the relative abundance of Streptococcus and Acinetobacter, and tended to increase (P = 0.082) dry matter digestibility. The BW of pigs fed SHWB was more uniform (P < 0.05) at the end of the 120 d study. Additionally, hot carcass weight of pigs fed SHWB tended to be more uniform (P = 0.089) than DDGS treatment. Conclusion Soybean hulls and wheat bran replacing DDGS in nursery diets improved uniformity of pigs at market weight, which might be attributed to beneficial modulation of the mucosa-associated microbiota and enhanced intestinal morphology during the nursery phase. Supplementation of NSPases had beneficial effects on the intestinal mucosa-associated microbiota, digestibility, and intestinal immunity in SHWB treatment, whereas no carryover effects were overserved at market weight.