Prevalent three-dimensional scaffolds for bone tissue engineering are mineralized collagen-hydroxyapatite (Col/HA) composites. Conventional mineralization techniques are either to coat collagen scaffold surfaces with minerals or to simply mix collagen and mineral nanoparticles together. These conventional in vitro collagen mineralization methods are different from the in vivo bone formation process and often result in scaffolds that are not suitable for bone tissue engineering. In this study, a unique perfusion-flow (i.e., dynamic) in conjunction with a previously described polymer-induced liquid-precursor (PILP) method was used to fabricate a porous Col/HA composite. The dynamic flow emulated the physiological extracellular fluid flow containing the mineralization ions, while the PILP method facilitated the deposition of the HA crystals within the collagen fibrils (i.e., intrafibrillar mineralization). By utilizing a dynamic PILP technique to mimic the in vivo bone formation process, the resultant Col/HA composite has a similar structure and compositions like human trabecular bone. A comparison of the dynamic and static mineralization methods revealed that the novel dynamic technique facilitates more efficient and homogenous mineral deposition throughout the Col/HA composite. The dynamic intrafibrillar mineralization method generated stiff Col/HA composites with excellent surface property for cell attachment and growth. The human mesenchymal stem cells cultured on the Col/HA composites quickly remodeled the scaffolds and resulted in constructs with an extensive cell-derived extracellular matrix network.