This study aimed to investigate the effects of soy protein concentrate (SPC) replacing animal protein supplements on modulation of mucosa-associated microbiota in relation to intestinal health of nursery pigs. Weaned pigs (n = 56; 6.4 ± 0.6 kg BW) were allotted to 5 treatments in a randomized complete block design (RCBD) with initial BW and sex as blocks and fed for 35 d in 3 phases (P1/2/3 for 10/12/13 d, respectively). Dietary treatments were NC (n = 12): a diet with fish meal 4/2/1%, poultry meal 10/8/4%, and blood plasma 4/2/1% for P1/2/3, respectively; RFM (n = 12): NC with SPC replacing fish meal; RPM (n = 12): NC with SPC replacing poultry meal; RBP (n = 12): NC with SPC replacing blood plasma, and PC (n = 8): NC with SPC replacing all animal protein supplements. All diets were formulated to meet the nutrient requirements by NRC (2012). On d 35, pigs were euthanized to collect jejunal mucosa to evaluate intestinal health and microbiota. PC increased (P < 0.05) Lactobacillaceae (1.04 to 8.15%), and tended to increase (P = 0.073) Prevotellaceae (7.48 to 18.94%), whereas it decreased (P < 0.05) Chao1 index (81.3 to 15.8), Helicobacteraceae (27.95 to 3.02), and tended to reduce (P = 0.099) Campylobacteraceae (2.95 to 0.13). RPM tended to increase (P = 0.090) Prevotellaceae (7.48 to 17.16%) and reduced (P < 0.05) Helicobacteraceae (27.95 to 11.02%) without affecting Chao 1. Decreased Chao 1 was correlated to reduced feed intake and therefore, weight gain of pigs.