Using three-dimensional (3D) bone engineering to fabricate bone segments is a better choice for repairing bone defects than using autologous bone. However, biomaterials for bone engineering are burdened with some clinical safety concerns. In this study, we layered commonly found clinical materials, hemostatic gelatin sponges, in a novel manner to create a 3D scaffold for bone engineering purposes. We further examined the comparable benefits of our design with both closed- and open-bottom holders. Cells in stacked layer disc systems were examined after a week of growth and differentiation. Osteoblasts in the outer layers of both closed- and open-bottom holder systems displayed gradually increased alkaline phosphatase (ALP) activity but decreased osteopontin (OPN) expression. Further, cell proliferation assays and LIVE/DEAD staining revealed decreased viable cell counts in the top layer with increased incubation time. However, while layered disc systems with closed-bottom holders underwent differentiation, they kept more differentiated cells alive within the gelatin sponge disc scaffold after 28 d of culturing. Whether cells were inoculated into the top, middle, or bottom portions of the layered disc stack, osteoblasts showed a preference for migrating to the top layer, in keeping with the oxygen and nutrients gradients. Regarding practical application, this study offers valuable information to promote the use of hemostatic gelatin sponges for bone engineering.