Introduction: Polyphenols, secondary metabolites synthesized by plants, are well known for their bioactive properties, including antioxidant, anti-inflammatory, and antimicrobial activities. Recently, their ability to modulate gut microbiota composition and functionality has gained increasing attention due to their potential impact on health and disease. The gut microbiota, critical for maintaining both intestinal and systemic health, can shift from eubiosis to dysbiosis, contributing to various diseases, such as metabolic disorders and chronic inflammation. In this context, plant-derived polyphenols offer promising interventions for restoring microbial balance and enhancing gut health. Methods: This study investigated the modulatory effects of polyphenols from two sources, propolis, and pomegranate, on gut microbiota composition and functionality through in vitro digestion and fermentation processes in both healthy and diseased conditions. Short-chain fatty acid (SCFA) profiles were quantified using chromatographic methods, and for propolis extract, changes in gut microbiota composition were assessed through 16S rRNA amplicon high-throughput sequencing (HTS). Results: The fermentation process demonstrated that pomegranate modulates gut microbiota functionality by significantly increasing SCFA production, mainly lactic acid, an essential precursor for their synthesis. Meanwhile, a standardized polyphenol mixture extracted from poplar-type propolis enhanced SCFA levels, including acetate, propionate, and butyrate. Propolis also promoted the growth of key SCFA-producing bacterial genera, such as Roseburia, Faecalibacterium, and Bifidobacterium. Conclusion: Both propolis and pomegranate exhibit distinct abilities to modulate gut microbiota composition and activity, highlighting their potential as prebiotic ingredients. These findings underscore the relevance of polyphenols in preventing and managing dysbiosis-related diseases, offering new insights for the development of functional foods and nutraceuticals.