Hypophosphatasia (HPP) is a hereditary musculoskeletal disorder caused by inactivating variants in the ALPL gene and subsequently reduced serum tissue-nonspecific alkaline phosphatase (TNSALP) activity. This inborn error of metabolism results in decreased bone quality, accumulations of osteoid, and reduced bone mineralization. Increased incidence of fractures and prolonged bone healing are characteristic features for HPP. Available enzyme replacement therapy (asfotase alfa), was reported to recover bone mineralization and bone quality in adult HPP patients. Moreover, it was shown that asfotase alfa improved fracture healing of former nonunions in two adult HPP patients. We hypothesized that the nonunions are filled partially with osteoid, offering great potential to benefit from the treatment with asfotase alfa to promote bone healing. In the present study, we report three adult patients with pediatric-onset HPP and detected ALPL-mutations with prolonged bone healing after arthrodesis, tibial stress fracture, and osteotomy. After the initiation of asfotase alfa, immediately increased levels of alkaline phosphatase (ALP) and bone-specific ALP, as well as decreased levels of pyridoxal-5-phosphate (PLP), were detected in biochemical analysis. Importantly, even after up to 5 years of non-healing, a progredient consolidation was shown, assessed by a custom three-dimensional evaluation of repeated cone-beam computed tomography (CBCT) images, characterized by rapidly increasing levels of bone volume per tissue volume (BV/TV) within the volume of interest (i.e., the region of the non-healing bone). These radiographical findings were in line with the reported restoration of functional ability and pain-free full weight-bearing, as well as increased neuromuscular parameters (e.g., improved muscle strength). Taken together, our findings indicate that asfotase alfa improves the osseous consolidation of nonunions likely due to re-mineralization of osteoid tissue filling the former gap and improving the functional ability in adult HPP patients, characterized by increasing levels of BV/TV assessed via an innovative three-dimensional evaluation of CBCT images.