In chronic kidney disease, as in many other diseases, dysbiosis of intestinal microbiota has been reported as a disturbance or imbalance of the normal microbiome content that could disrupt the symbiotic relationship between the host and associated microbes, a disruption that can result in diseases. The disruption of gut barrier function allows the translocation of endotoxins and bacterial metabolites to the organism, thus contributing to uremic toxicity, inflammation and progression of chronic kidney disease. Increased intake of some nutrients and different nutritional strategies have been proposed to modulate gut microbiota, thus offering the opportunity for therapeutic interventions modifying the diet, decreasing uremic toxins production, increasing toxin excretion and finally modifying the normal microbiome content. The use of probiotics, prebiotics and low protein diets, among other approaches, could also improve this imbalance and/or decrease permeability of the intestinal barrier. In this review, the link between nutrients, microbiota and uremic toxins with chronic kidney disease progression has been studied thoroughly. Furthermore, this review outlines potential mechanisms of action and efficacy of probiotics, prebiotics and low protein diets as a new chronic kidney disease management tool.