The loss-of-function mutations in the ALPL result in hypophosphatasia (HPP), an inborn metabolic disorder that causes skeletal mineralization defects. In adults, the main clinical features are early loss of primary or secondary teeth, osteoporosis, bone pain, chondrocalcinosis, and fractures. However, guidelines for the treatment of adults with HPP are not available. Here, we show that ALPL deficiency caused a reduction in intracellular Ca 2+ influx, resulting in an osteoporotic phenotype due to downregulated osteogenic differentiation and upregulated adipogenic differentiation in both human and mouse bone marrow mesenchymal stem cells (BMSCs). Increasing the intracellular level of calcium in BMSCs by ionomycin treatment rescued the osteoporotic phenotype in alpl +/− mice and BMSC-specific (Prrx1-alpl −/−) conditional alpl knockout mice. Mechanistically, ALPL was found to be required for the maintenance of intracellular Ca 2+ influx, which it achieves by regulating L-type Ca 2+ channel trafficking via binding to the α2δ subunits to regulate the internalization of the L-type Ca 2+ channel. Decreased Ca 2+ flux inactivates the Akt/GSK3β/β-catenin signaling pathway, which regulates lineage differentiation of BMSCs. This study identifies a previously unknown role of the ectoenzyme ALPL in the maintenance of calcium channel trafficking to regulate stem cell lineage differentiation and bone homeostasis. Accelerating Ca 2+ flux through L-type Ca 2+ channels by ionomycin treatment may be a promising therapeutic approach for adult patients with HPP.