Chronic kidney disease (CKD) is a worldwide health problem, because it is one of the most common complications of metabolic diseases including obesity and type 2 diabetes. Patients with CKD also develop other comorbidities, such as hypertension, hyperlipidemias, liver and cardiovascular diseases, gastrointestinal problems, and cognitive deterioration, which worsens their health. Therapy includes reducing comorbidities or using replacement therapy, such as peritoneal dialysis, hemodialysis, and organ transplant. Health care systems are searching for alternative treatments for CKD patients to mitigate or retard their progression. One new topic is the study of uremic toxins (UT), which are excessively produced during CKD as products of food metabolism or as a result of the loss of renal function that have a negative impact on the kidneys and other organs. High urea concentrations significantly modify the microbiota in the gut also, cause a decrease in bacterial strains that produce anti-inflammatory and fuel molecules and an increase in bacterial strains that can metabolize urea, but also produce UT, including indoxyl sulfate and p-cresol sulfate. UT activates several cellular processes that induce oxidative environments, inflammation, proliferation, fibrosis development, and apoptosis; these processes mainly occur in the gut, heart, and kidney. The study of the microbiota during CKD allowed for the implementation of therapy schemes to try to reduce the circulating concentrations of UT and reduce the damage. The objective of this review is to show an overview to know the main UT produced in end-stage renal disease patients, and how prebiotics and probiotics intervention acts as a helpful tool in CKD treatment.