The application of bone graft substitutes with osteoinductive properties is of high importance for the repair of large bone defects. COLLOSS® E, a protein lyophilizate extracted from equine long bones, exhibits an osteoinductive potential which has been proven in several studies. In this work, a mechanically stable, but biodegradable support for COLLOSS® E has been developed aiming at a bone graft substitute that retains shape and size when coming in contact with body fluids. Mineralization of collagen type I, isolated from horse tendon, resulted in a stable collagen hydroxyapatite nanocomposite. By means of freeze drying, this composite was used to prepare 3D scaffolds which can be filled with the cotton-wool like COLLOSS® E material. These scaffolds exhibit a porous microstructure and a good mechanical stability in dry and wet state. Cell culture experiments with human bone marrow stromal cells (hBMSC) revealed the cytocompatibility of the newly developed composite material. Cells were able to adhere, proliferate and differentiate into the osteoblastic lineage. The osteoinductive nature of COLLOSS® E has been demonstrated by a significant higher activity of the osteogenic marker alkaline phosphatase (ALP) on combined scaffolds (mineralized collagen scaffolds filled with COLLOSS® E) compared to pure scaffolds. The combination of COLLOSS® E with scaffolds made of a collagen hydroxyapatite composite results in a synthetic bone graft substitute which can be completely remodelled into vital bone tissue opening an interesting new possibility for the therapy of bone defects.