Coffee, the second most consumed beverage globally after water, contains a complex mixture of bioactive compounds, including caffeine, polyphenols, and melanoidins, which contribute to its diverse physiological effects. Epidemiological studies suggest that coffee consumption is associated with reduced risks of chronic kidney disease (CKD), kidney stones, and kidney cancer. Meta-analyses have reported a 14–28% lower risk of CKD progression, kidney failure, or CKD-related mortality among regular coffee drinkers. Similarly, Mendelian randomization studies indicate a protective role of coffee and caffeine against kidney stone formation, with higher intake linked to a significantly lower risk. Research also suggests an inverse relationship between coffee consumption and renal cell carcinoma, particularly among never-smokers, though regional and methodological differences contribute to variability in findings. Despite these potential benefits, coffee intake must be carefully managed in individuals with advanced kidney disease or on dialysis, as caffeine can transiently elevate blood pressure, and additives like milk or creamers may increase potassium and phosphorus intake. While coffee’s health effects are influenced by genetic and metabolic factors, emerging evidence supports its role in kidney health. Further randomized controlled trials are needed to clarify the underlying mechanisms and refine dietary recommendations for individuals at risk of kidney-related complications.