Uremic toxins are biologically active compounds that accumulate in patients with chronic kidney disease (CKD), contributing to various complications, including cardiovascular dysfunction, neurotoxicity, and inflammation. Among these toxins, protein-bound uremic toxins (PBUTs) such as phenol, indoxyl sulfate, and p-cresyl sulfate are particularly problematic due to their poor clearance by conventional dialysis. Recent studies have identified dietary polyphenols, including quercetin and gallic acid derivatives, as potential inhibitors of bacterial enzymes responsible for PBUT production in the gut. This chapter reviews the classification, sources, and pathophysiological effects of uremic toxins and highlights recent advances in the inhibition of gut microbial enzymes such as tyrosine phenol-lyase (TPL) and tryptophan indole-lyase (TIL) by functional food components. These findings offer novel preventive strategies for CKD management and improvement of quality of life through microbiota-targeted nutritional interventions.