Phosphate overload contributes to mineral bone disorders that are associated with crystal nephropathies. Phytate, the major form of phosphorus in plant seeds, is known as an indigestible and of negligible nutritional value in humans. However, the mechanism and adverse effects of high-phytate intake on Ca²⁺ and phosphate absorption and homeostasis are unknown. Here, we show that excessive intake of phytate along with a low-Ca²⁺ diet fed to rats contributed to the development of crystal nephropathies, renal phosphate wasting, and bone loss through tubular dysfunction secondary to dysregulation of intestinal calcium and phosphate absorption. Moreover, Ca²⁺ supplementation alleviated the detrimental effects of excess dietary phytate on bone and kidney through excretion of undigested Ca²⁺-phytate, which prevented a vicious cycle of intestinal phosphate overload and renal phosphate wasting while improving intestinal Ca²⁺ bioavailability. Thus, we demonstrate that phytate is digestible without a high-Ca²⁺ diet and is a risk factor for phosphate overloading and for the development of crystal nephropathies and bone disease.