Human pluripotent stem cells such as embryonic stem cells (hESCs) and multipotent stem cells like mesenchymal stem cells (hMSCs) hold great promise as potential cell sources for bone tissue regeneration. Comparing the in vivo osteogenesis of hESCs and hMSCs by biomaterial-based cues provides insight into the differentiation kinetics of these cells as well as their potential to contribute to bone tissue repair in vivo. Here, we compared in vivo osteogenic differentiation of hESCs and hMSCs within osteoinductive calcium phosphate (CaP)-bearing biomineralized scaffolds that recapitulate a bone-specific mineral microenvironment. Both hESCs and hMSCs underwent osteogenic differentiation responding to the biomaterial-based instructive cues. Furthermore, hMSCs underwent earlier in vivo osteogenesis compared to hESCs, but both stem cell types acquired a similar osteogenic maturation by 8 weeks of implantation.