Red beetroot is a well-recognized and established source of bioactive compounds (e.g., betalains and polyphenols) with anti-inflammatory and antimicrobial properties. It is proposed as a potential alternative to zinc oxide with a focus on gut microbiota modulation and metabolite production. In this study, weaned pigs aged 28 days were fed either a control diet, a diet supplemented with zinc oxide (3000 mg/kg), or 2% and 4% pulverized whole red beetroot (CON, ZNO, RB2, and RB4; respectively) for 14 days. After pigs were euthanized, blood and digesta samples were collected for microbial composition and metabolite analyses. The results showed that the diet supplemented with red beetroot at 2% improved the gut microbial richness relative to other diets but marginally influenced the cecal microbial diversity compared to a zinc-oxide-supplemented diet. A further increase in red beetroot levels (4%-RB4) led to loss in cecal diversity and decreased short chain fatty acids and secondary bile acid concentrations. Also, an increased Proteobacteria abundance, presumably due to increased lactate/lactic-acid-producing bacteria was observed. In summary, red beetroot contains several components conceived to improve the gut microbiota and metabolite output of weaned pigs. Future studies investigating individual components of red beetroot will better elucidate their contributions to gut microbiota modulation and pig health.