<p>This study reviews the multifaceted health effects of <i>Allium</i>-derived compounds, focusing on their interaction with gut microbiota and the subsequent influence on gut homeostasis, metabolic health, inflammation, and disease states. <i>Allium</i>-derived compounds, such as polysaccharides, flavonols, and sulfur-containing compounds, i.e., allicin, are present in <i>Allium</i> that function as prebiotics to modulate gut microbiota composition and further exert systemic effects on metabolic disorders. The prebiotic effects of inulin-fructosaccharides, sulphur compounds, and flavonols, and their capacity to enhance gut health through fermentation processes and short-chain fatty acid (SCFA) production are explored. The review presents findings from several animal studies exploring the phytogenic properties of <i>Allium</i> species and their associated gut-mediated benefits. The study also touches on emerging research that explores several approaches to incorporate <i>Allium</i> or its metabolites in various formulations, such as in nano-based structures, high-pressure processing, or combining it with probiotics. Such approaches aim to enhance <i>Allium</i> nutraceutical and its gut interaction benefits. Finally, this comprehensive analysis highlights the crucial role of gut microbiota as a mediator in the health benefits of <i>Allium</i> phytochemicals, paving the way for the broader utilisation of this primary dietary source in nutraceuticals and for future needed studies and potential clinical applications.</p> Graphical Abstract <p></p>