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Gut dysbiosis refers to an imbalance in gut microbiota composition and function. <i>Opuntia ficus-indica</i> extract has been shown to modulate gut microbiota by improving SCFA production in vivo and gastrointestinal discomfort (GD) in humans. The aim of this study was to demonstrate the efficacy of Odilia^TM on gastrointestinal health by changing the microbial diversity of species involved in inflammation, immunity, oxidation, and the brain–gut–muscle axis. A randomized, double-blind clinical trial was conducted in 80 adults with gut dysbiosis. The intervention consisted of a 300 mg daily intake of Odilia^TM (n = 40) or maltodextrin as a placebo (n = 40), administered for 8 weeks. Intervention effect was evaluated using 16S metagenomics and GIQLI/GSAS scores at baseline, at 4 and 8 weeks. Eight weeks of Odilia^TM supplementation positively modulates gut microbiota composition with a significant reduction in the <i>Firmicutes</i> to <i>Bacteroidetes</i> ratio (<i>p</i> = 0.0012). Relative abundances of beneficial bacteria (<i>Bacteroides</i> and <i>Clostridium_XIVa</i>) were significantly increased (<i>p</i> < 0.001), in contrast to a significant reduction in pro-inflammatory bacteria (<i>p</i> < 0.001). Accordingly, GIQLI and GSAS scores revealed successful improvement in GD. Odilia^TM may represent an effective and well-tolerated treatment in subjects with gut dysbiosis.