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Abstract Chronic kidney disease (CKD) results mainly from diabetes, hypertension, and glomerulonephritis, which can develop into end‐stage renal disease and CKD‐related complications, thereby causing high morbidity and mortality. This progression is correlated with pathogenic alterations in the gut microbiota that generate uremic toxins, mainly including indoxyl sulfate, p‐cresol sulfate, and trimethylamine‐N‐oxide. The uremic toxins directly or indirectly induce CKD through oxidative stress, inflammatory response, and subsequently renal fibrosis. However, ongoing developments in CKD therapy still lack nutritional guidelines and new pharmacotherapies with significant effects. In this review, we discuss the modulatory effects of plant‐derived bioactive ingredients, such as dietary fiber (oligosaccharides and polysaccharides), polyphenols (e.g., curcumin, anthocyanins, catechins, and resveratrol), and peptides, on gut microbiota and CKD particularly from the view of the gut–kidney axis. We believe that a comprehensive understanding of the underlying mechanisms of CKD is necessary to develop new targeted therapy strategies that will benefit the prevention and treatment of CKD.