Recently soybean meal (SBM) has garnered more attention due to its increased feeding value during periods of stress and improved bioavailable energy. However, the influence of the innate bioactive compounds in SBM on the microbiome and fermentation products have not been fully elucidated. Thus, the experimental objective was to investigate the mechanism of action of SBM and its bioactive compounds in the gastrointestinal tract of nursery pigs. Two replications of 18 barrows (8.12 ± 0.80 kg BW; PIC800 × Camborough; N=36), were randomly assigned to a dietary treatment of either a high SBM positive control (SBMC; 28.6%), a negative control void of SBM (SP), but included soy protein isolate and concentrate to provide amino acids from soy protein the same as SBM in SBMC; SP formulated to the same contribution and composition of isoflavones as SBMC (SP+ISO; 528 mg/kg of soy-isoflavones); SP diet fortified with soybean functional lipids of lecithin and phytosterols at similar concentration in SBMC (SP+LIP; 2.85 g/kg of functional lipids); SP formulated to the same contribution and ratio of insoluble to soluble fiber as SBM in SBMC (SP+FIB; 30 g/kg of soy fiber); or SP diet fortified with lunasin peptide at 3.81 g/kg (SP+LUN). Pigs were individually housed, and limit fed 2.5 times maintenance for a metabolism study consisting of a 6-d adaptation period, followed by 72-h of urine and fecal collections. On d 12, pigs were necropsied, and ileal, cecal, and colonic digesta were collected for immediate short-chain fatty acid (SCFA) analysis. The pH of ileal and cecal digesta were also collected. Data were analyzed as a linear mixed model with treatment as a fixed effect, replicate as a random effect, and initial BW as a covariate where appropriate using PROC MIXED in SAS 9.4. The pH of both ileal (P=0.478) and cecal (P=0.874) digesta did not differ among treatments. Relative to SP, pigs fed SP+FIB and SBM had a 97.8% and 63.4% increase in acetate production, respectively (P=0.012). Similarly, pigs fed SP+FIB and SBM had increased total SCFA concentration in the ileum (P=0.016), but there was no difference among treatments for propionate or butyrate production (P>0.05). The molar proportion of butyrate was increased in the cecum in pigs fed SBMC and SP+FIB (P<0.01), which increased the total concentration (mM/g) of SCFA in the cecal digesta (P<0.05). The SP+FIB treatment had increased concentration (mM/g) and molar proportion of butyrate produced in the colon (P<0.01). While pigs fed SBMC and SP had increased molar proportion of propionate in the colon (P<0.05), total colonic SCFA concentration did not differ (P>0.05).