Amorphous calcium phosphate (ACP) has shown significant effects on the biomineralization and promising applications in bio-medicine. However, the limited stability and porosity of ACP material restrict its practical applications. A storage stable highly porous ACP with Brunauer–Emmett–Teller surface area of over 400 m2/g was synthesized by introducing phosphoric acid to a methanol suspension containing amorphous calcium carbonate nanoparticles. Electron microscopy revealed that the porous ACP was constructed with aggregated ACP nanoparticles with dimensions of several nanometers. Large angle X-ray scattering revealed a short-range atomic order of <20 Å in the ACP nanoparticles. The synthesized ACP demonstrated long-term stability and did not crystallize even after storage for over 14 months in air. The stability of the ACP in water and an α-MEM cell culture medium were also examined. The stability of ACP could be tuned by adjusting its chemical composition. The ACP synthesized in this work was cytocompatible and acted as drug carriers for the bisphosphonate drug alendronate (AL) in vitro. AL-loaded ACP released ~25% of the loaded AL in the first 22 days. These properties make ACP a promising candidate material for potential application in biomedical fields such as drug delivery and bone healing.