Abstract This study aims to investigate the impact of various levels of soy protein concentrate (SPC) replacing conventional soybean meal (SBM) on various parameters related to intestinal health and growth performance of nursery pigs under F18+ Escherichia coli challenge. Newly weaned pigs [n = 72; initial body weight (BW) = 6.6 ± 0.3 kg] were randomly allotted to 6 treatment groups based on randomized complete block design with initial BW and sex as blocks and fed for 25 d (P1/2 for 11/14 d, respectively). The treatment groups were 1) NC: a diet with conventional SBM, 2) PC: NC with F18+ E. coli challenge at d 7 (2.1 × 1010 CFU); 3) T1: PC with 5% SPC replacing conventional SBM; 4) T2: PC with 10% SPC replacing conventional SBM; 55) T3: NC with 10% SPC replacing conventional SBM, and 6) AGP: PC with 0.25% bacitracin methylene disalicylate. At the end of study, all pigs were euthanized to collect jejunal tissues to measure parameters related to intestinal health. Data were analyzed using MIXED procedure in SAS. The PC decreased (P < 0.05) average daily gain (ADG) and average daily feed intake (ADFI) on d 7 to d 25 (post-challenge) compared with NC. The T2 decreased (P < 0.05) ADG and ADFI on post-challenge period compared with T3. The ADG tended to linearly decrease (P = 0.067) and ADFI linearly decrease (P < 0.05) on post-challenge period with increasing SPC supplementation replacing SBM in the diets. The E. coli challenge increased (P < 0.05) fecal score in PC, and T2 treatments compared with NC, and T3, respectively. The tumor necrosis factor-alpha (TNF-α) in jejunal mucosa linearly increased (P < 0.05) with increasing SPC supplementation replacing SBM in nursery diets under E. coli challenge. The PC decreased (P < 0.05) interleukin-8 (IL-8) compared with NC. The PC (P = 0.078) and T3 (P = 0.099) tended to decrease immunoglobulin A (IgA) compared with NC. The AGP increased (P < 0.05) IgA compared with PC. The AGP increased (P < 0.05) the expression of occludin (OC) compared with PC. The expression of OC tended to linearly decrease (P = 0.099) with increasing SPC supplementation replacing SBM in nursery diets under E. coli challenge. The T2 increased (P < 0.05) villus height to crypt depth ratio (VH:CD) compared with T3. In conclusion, supplementation of SPC replacing SBM in the diet did not alleviate the deleterious effect of E. coli challenge on growth performance nursery pigs, which might be contributed by reduced feed intake. Additionally, supplementation of SPC seems to exacerbate the negative effect of E. coli challenge with increased intestinal inflammation and intestinal disintegration.