Nanoscale replication of the hierarchical organization of minerals in biogenic mineralized tissues is believed to contribute to the better mechanical properties of biomimetic collagen scaffolds. Here, an intrafibrillar nanocarbonated apatite assembly is reported, which has a bone-like hierarchy, and which improves the mechanical and biological properties of the collagen matrix derived from fibril-apatite aggregates. A modified biomimetic approach is used, which based on the combination of poly(acrylic acid) as sequestration and sodium tripolyphosphate as templating matrix-protein analogs. With this modified dual-analog-based biomimetic approach, the hierarchical association between collagen and the mineral phase is discerned at the molecular and nanoscale levels during the process of intrafibrillar collagen mineralization. It is demonstrated by nanomechanical testing, that intrafibrillarly mineralized collagen features a significantly increased Young's modulus of 13.7 ± 2.6 GPa, compared with pure collagen (2.2 ± 1.7 GPa) and extrafibrillarly-mineralized collagen (7.1 ± 1.9 GPa). Furthermore, the hierarchy of the nanocarbonated apatite assembly within the collagen fibril is critical to the collagen matrix's ability to confer key biological properties, specifically cell proliferation, differentiation, focal adhesion, and cytoskeletal arrangement. The availability of the mineralized collagen matrix with improved nanomechanics and cytocompatibility may eventually result in novel biomaterials for bone grafting and tissue-engineering applications.