Interactions between the gut microbiota and intestinal barrier may contribute to the pathophysiology of high-altitude illnesses. This study aimed to determine the effects of targeting the gut microbiota using dietary supplementation with a blend of fermentable fibers and polyphenol sources on gut microbiota composition, fecal short-chain fatty acids (SCFAs), and intestinal function and permeability during hypobaric hypoxia exposure. Healthy adults participated in a randomized, placebo-controlled, crossover study. Food products containing oligofructose-enriched inulin, galacto-oligosaccharide, high-amylose corn starch, cocoa, green tea and cranberry extracts, and blueberry powder (FP) or maltodextrin (placebo; PL) were consumed daily during three 2-wk phases separated by a >=1-wk washout. During the final 36 h of each phase, participants resided in a hypobaric chamber simulating low (LA; 500 m) or high (HA; 4,300 m) altitude creating three experimental conditions: PL + LA, PL + HA, and FP + HA. Twenty-six participants completed >=1 study phase and 13 [12 male; 21 +- 3 yr; body mass index (BMI) 25.4 +- 2.4 kg/m2] completed all three phases. Results demonstrated that FP mitigated hypoxia-induced increases in intestinal permeability within the small intestine and proximal colon while increasing Bifidobacterium relative abundance and decreasing gut microbiota alpha -diversity and colonic pH. Higher Bifidobacterium relative abundance and lower colonic pH were associated with greater reductions in intestinal permeability. However, FP did not alter fecal SCFA concentrations and increased gastrointestinal symptoms and altitude sickness during hypobaric hypoxia exposure. Findings suggest that targeting the gut microbiota with a combination of fermentable fibers and polyphenols can prevent hypobaric hypoxia-induced increases in intestinal permeability but that benefit does translate into a reduction in altitude illness symptoms.