Background Bone tissue engineering emerged as a practical approach to tackle the prosthetic industry limitations. Merging aspects from developmental biology, engineering and medicine with the aim to produce fully-functional bone tissue. Mesenchymal stem cells (MSCs) harbor the capability of self-renewal and specific lineage differentiation. Herein lies their potential for bone tissue engineering. Among MSCs, human dental pulp stem cells (hDPSCs) lodge higher proliferation rate, shorter doubling times, lower cellular senescence, and enhanced osteogenesis than hBM-SCs. In addition, these cells have ease in access and a subtle extraction procedure. Thus, harbouring fewer moral concerns than most MSCs available and embodying a promising cell source for BTE therapies able to replace hBM-MSCs. Interestingly, their study has been limited. Conversely, there is a need for their further study to harness their BTE true value, with special emphasis in the design of bioprocesses able to produce viable, homogenous bone constructs in a clinical scale. Methods Here, we study the in vitro osteogenic differentiation of hDPSCs encapsulated in alginate hydrogels under suspended culture in a novel and scalable perfusion bioreactor, establishing culture conditions; and compare it with three-dimensional (3D) static and fed-batch culture. Results hDPSC-based bone-like constructs produced in the novel system performed above the compared culture strategies, displaying higher alkaline phosphatase activity, more homogeneous, denser and functional bone constructs. In addition, cell constructs produced by the in-house designed system were richer in mature osteoblasts. Conclusion This study reports the development of a novel bioprocess able to produce hDPSC-alginate-based bone-like constructs to be used as bone fillers, while providing new insights into hDPSCs therapeutic potential and a system able to be transferred from the laboratory bench into medical facilities.