The objective was to evaluate the prebiotic effects of a milled whole cranberry beverage on modulating the gut microbiota in young adults. Adults (n = 17; ages 18–42 y; BMI 30.5 ± 3.1 kg/m2) were enrolled in a 60-d, two-period, randomized, placebo-controlled, crossover clinical study. Throughout the study, participants were fed a standardized 10-d cycle menu on site. During each 20-d treatment period, participants consumed twice daily a whole cranberry or placebo beverage (240 mL per serving). Treatment periods were separated by an 11-wk washout period and preceded by 10-d run-in periods on the controlled study diet. Fecal samples were collected before and after the dietary intervention for bacterial compositional analysis and short-chain fatty acid analysis by LC-MS/MS. The V5-V6 region of the 16S rRNA gene in fecal DNA was amplified and sequenced. Taxonomy was assigned using the q2-feature-classifier in QIIME2 and matched against the Greengenes 13_8 database. Differential abundance was analyzed using ANCOM2 in R. Alpha-diversity was assessed using Faith’s PD, Shannon diversity, and observed OTU richness generated by QIIME 2 and compared between treatments using Mann-Whitney U test. Beta-diversity was compared between treatments using PERMANOVA of the weighted and unweighted UniFrac distances between samples generated by QIIME 2. Coriobacteriaceae was significantly more abundant after participants consumed the cranberry as compared with the placebo beverage (ANCOM W > 0.7). The clinically-important pathogen Clostridium perfringens was present after consumption of the placebo beverage, but was a structural zero (not present) after consumption of the cranberry beverage. Alpha-diversity, beta-diversity, and fecal short-chain fatty acid concentrations did not differ between treatments. Daily consumption of a whole cranberry beverage resulted in favorable change in the composition of the gut microbiota and thus showed prebiotic potential.