Mineral ion regulation and vitamin D activation are closely interconnected processes that are vital for maintaining overall health, particularly in terms of bone metabolism and calcium (Ca+2) homeostasis. Mineral formation pathways involve the uptake of ions from the environment, the transport of ions by cells, sometimes temporary storage, and ultimately deposition inside or outside the cells. Minerals and trace elements are crucial micronutrients with recognized biochemical and biological roles. Insufficiency in these micronutrients is related to extensive human illnesses. This highlights the physiopathological aspects of the hormone-mediated control of biomineralization. Several component systems that affect bone formation, maintenance, and nutritional health, including the functions of Ca+2, inorganic phosphate (Pi), dietary intake, and the renal excretion of minerals, are also highlighted. Additionally, there is an elusive balance between activators and inhibitors of mineralization, such as phosphorus (PO4−3), ionized Ca+2, and pyrophosphate. Moreover, this chapter summarizes the significant importance of restricted regulation of serum Ca+2 and PO4−3 levels in numerous biological processes, i.e., parathyroid hormone (PTH), vitamin D, vitamin K, and fibroblast growth factor 23 (FGF23). Finally, this chapter highlights the physiology and pathophysiological findings, clinical characteristics, and treatments.