This study investigated whether the inclusion of a stimbiotic (STB) can improve performance, influence intestinal microbiota and fermentation activity, and reduce pro-inflammatory cytokines in piglets fed a low zinc oxide diet without antimicrobial growth promotors compared to fructo-oligosaccharide (FOS) and mannan-oligosaccharide (MOS) when housed either in good sanitary (GS) or poor sanitary (PS) environments. One hundred forty-four male pigs (28-day-old) were sorted by initial body weight (BW) and allocated to one of six experimental treatments: 1) GS environment without any additive (GS-CTR); 2) GS environment with 0.01% stimbiotic (GS-STB); 3) PS environment (without cleaning and disinfection of a previously populated room) without any additive (PS-CTR); 4) PS environment with 0.01% STB (PS-STB); 5) PS environment with 0.1% MOS (PS-MOS); and 6) PS environment with 0.2% FOS (PS-FOS). Each treatment had six replicates, with four animals each. Three feeding phases, based on corn, wheat, and soybean meal were available ad libitum for the 42-days of the study. Housing piglets under PS conditions negatively influenced performance, increased plasma tumor necrosis factor alpha (TNF-α), affected the fecal microbial populations and increased concentrations of branched-chain fatty acids (BCFA) compared to GS. Stimbiotic improved 42-d-BW under PS conditions (P < 0.05) whereas MOS or FOS had no effect. On d35, plasma TNF-α was reduced with STB in PS (P < 0.05). The ratio between VFA:BCFA increased (P < 0.05) with STB, MOS or FOS in PS, and under GS condition, STB also increased the ratio. Stimbiotic increased the proportion of Clostridiales Family XIII Incertae Sedis and Clostridiaceae, while MOS and FOS increased Selenomonadaceae, Catabacteriaceae and Fibrobacteraceae. These results indicate that STB shifted the intestinal microbiome to favor fiber fermentation which likely contributed to reduced inflammatory response and improved performance, particularly in piglets reared in PS conditions.