Chronic kidney disease (CKD) has been a constant burden worldwide, with a prevalence of more than 10% of the population and with mortality reaching 1.2 million deaths and 35.8 million disability-adjusted life years (DALYs) in 2017, as it is claimed by the Global Burden of Diseases. Moreover, an increase in its prevalence is expected in the next years due to a rise in the number of people suffering from obesity, diabetes mellitus and hypertension. On the other hand, with cardiovascular morbidity and mortality showing a downward trend, maybe it is time to focus on CKD, to minimize the preventable risk factors involved in its progression toward end-stage kidney disease (ESKD) and to offer a better quality of life. Another major health burden is represented by infectious diseases, particularly urinary tract infections (UTIs), as it is considered that approximately 40–50% of women and 5% of men will have at least one episode during their lifetime. Additionally, CKD consists of a constellation of immunological and metabolical disturbances that lead to a greater risk of UTIs: increased apoptosis of lymphocytes, elevated levels of tumor necrosis factor α and interleukin 6, which lower the function of neutrophils and increased levels of uremic toxins like p-cresyl sulfate and indoxyl sulfate, which alter the adherence and migration of leukocytes to the sites of injury. Moreover, UTIs can lead to a more rapid decline of kidney function, especially in stages G3-G5 of CKD, with all the complications involved. Last, but not least, antibiotherapy is often complicated in this category of patients, as antibiotics can also negatively affect the kidneys. This review will try to focus on the particularities of the urinary microbiome, asymptomatic bacteriuria and UTIs and the subtle balance between the risks of them and the risks of antibiotherapy in the evolution of CKD.