Background: Dietary fiber confers numerous health benefits, potentially mediated by the gut microbiota. Most people do not consume enough dietary fiber despite the emphasis in current guidelines. Making personalized recommendations for fiber sources that provide specific benefits through microbiome modulation may be beneficial. However, the mechanisms by which fiber from different whole food sources differentially affects gut microbiota are incompletely understood. Objective:The purpose of this pilot study is to evaluate the impact of fiber from exclusively whole grains (WG) or fruits and vegetables (FV) on microbiome composition and microbial metabolites associated with metabolic health. Methods: Healthy individuals with a BMI between 25-30 who habitually consumed less than the USDA-recommended dietary fiber amount were enrolled in a 12-week crossover dietary intervention. Participants were instructed to consume the provided WG or FV foods for 4 weeks, including a 1-week ramp-up, to increase daily fiber intake to 32 grams. Fiber intake was assessed using the Automated Self-Administered 24-hour dietary assessment tool. The primary outcome was alterations in body weight and body fat percentage. Secondary outcomes included alterations in gut microbial composition and fecal metabolite concentrations. Stool samples were collected at baseline and at the end of each week. The V4 region of 16S rRNA was sequenced to determine changes in gut microbial composition, and targeted metabolomics was used to analyze fecal metabolite concentrations (short-chain fatty acids, sterols, bile acids, and amino acids). Results: Both WG (n = 16) and FV (n = 15) increased daily energy-adjusted dietary fiber intake (g/1000kcal) from baseline to week 4 (4.1g and 9.6g, respectively) but did not alter body weight and fat percentage. WG and FV foods increased alpha diversity by week 3 (ß = 0.75 ± 0.21, p < 0.01; ß = 0.99 ± 0.40, p = 0.03, respectively). WG correlated with a decrease in Monoglobacaea and Megasphaeraceae abundance, while FV intake correlated with increases in Lachnospira, Agathobacter, and Bacteroidaceae abundance (adjusted p-value < 0.25). Fecal concentrations of cholesterol (ß = -0.87 ± 0.22, p < 0.01) and branch-chain amino acids (ß = -0.40 ± 0.18, p = 0.04) decreased with WG food consumption, while FV increased butyrate (ß = 0.77 ± 0.28, p = 0.02) and decreased primary bile acids (ß = -1.48 ± 0.66, p = 0.04) and gamma-aminobutyrate concentrations (ß = -4.29 ± 1.21, p < 0.01). Conclusion: WG and FV foods increased alpha diversity, altered taxa abundances, and had distinct effects on microbial metabolites associated with metabolic health. These results suggest that WG versus FV beneficially influence microbial metabolites in different ways, suggesting potential strategies for personalizing dietary fiber recommendations.