Chronic kidney disease-mineral bone disorder (CKD-MBD) is a systemic disorder characterized by altered mineral and bone metabolism. The role of PHOSPHO1 and tissue-nonspecific alkaline phosphatase (TNAP) in controlling bone mineralization in CKD-MBD is unclear. We utilized the adenine-induced murine model of CKD-MBD in which mice present with hyperphosphatemia, hyperparathyroidism, and elevated FGF23 levels, and bone turnover markers. Micro-CT and histomorphometric analysis revealed microarchitectural changes to the trabecular and cortical bone of CKD mice. Furthermore, CKD cortical bone mineral density (BMD) was increased (p < 0.05) whereas CKD trabecular bone BMD was decreased (p < 0.05). These changes were accompanied by decreased Alpl mRNA expression (p < 0.001) and increased Phospho1 mRNA expression (p < 0.01) in CKD bones, which were confirmed at the protein level. Cortical bone BMD was unchanged in Phospho1 knockout (P1KO) CKD mice suggesting that the increased cortical BMD noted in CKD was driven by the increased PHOSPHO1 expression. Intriguingly, other structural parameters were improved in P1KO CKD mice. In an attempt to determine the causes of the mineralization defects noted in the CKD mice, we investigated the direct effects of FGF23, PTH, and phosphate (Pi) administration on PHOSPHO1 and TNAP expression by primary murine osteoblasts. PHOSPHO1 and TNAP expression were down-regulated in a concentration-dependent manner by Pi and PTH whereas the effects of FGF23 treatment, with or without klotho, were less marked. Osteoblast matrix mineralization was increased with Pi, decreased with PTH in a concentration-dependent manner and FGF23 had no effect. In summary, this pre-clinical model of CKD presented with hypomineralization of trabecular bone but hypermineralisation of cortical bone. Similarly, divergent expression levels of TNAP and PHOSPHO1 were noted in CKD. These novel observations implicate these key phosphatases in the etiology of CKD-MBD and may help explain the disordered skeletal mineralization characteristic of this progressive disorder.