Disorders influencing bone form a major burden worldwide, with osteoporosis being the most common fracture-inducing bone disease. Currently, animal models are being utilized to develop and screen novel treatments. However, due to interspecies variations, different microenvironments, and ethical considerations, there is a need for a complex 3D bone model. This research aimed to perform a pilot study on developing a standardized representative bone model using a perfusion-based bioreactor, and to characterize the overall 3D bone proteomic profile. An immortalized human fetal osteoblastic cell line (hFOB1.19) was seeded on collagen scaffolds and cultured for 21 days in a perfusion bioreactor system and in static cultures. Different analyses allowed the monitoring of cell viability and compared morphological and proteome differences between both conditions. Scanning electron microscopy images suggested an altered cellular morphology within the bioreactor culture compared to the static cultures. A proteomic analysis identified a total of 1897 proteins and a total of 93 unique regulated proteins. Enrichment analyses of these proteins revealed seven significant pathways including TNF-alpha signaling pathway via NF-kB. These pathways also included hypoxia and epithelial-mesenchymal transition, where the EMT pathway was the most significant and indicated a reduction in cell motility within the bioreactor system on day 21. This preliminary study suggests that the U-CUP perfusion bioreactor is promising for further exploration of facilitating osteogenic differentiation induction in 3D cultures.