The treatment of osteochondral defects is a major topic of current research and has become more important in our aging society. The challenges in bone and cartilage repair arise from the structure and function of these different tissues. This study proposes a biphasic model combining cartilage and bone scaffolds based on silk fibroin (SF) biopolymers. For the cartilage phase, SF scaffolds were coated with gelatin and/or agarose layers. For bone scaffolds, mineralized collagen solutions were coated on or mixed into the SF matrix. The physical and biological properties of these samples were evaluated to find the optimum conditions for a biphasic scaffold. Modification of both cartilage and bone scaffolds resulted in a smaller pore size, lower swelling rate, and higher rigidity. Gelatin significantly promoted cartilage biomarker production and agarose facilitated cell proliferation, inducing a homogeneous cell distribution and stimulating chondrogenesis. Furthermore, modification with mineralized collagen decreased cell proliferation in osteoblast progenitors but enhanced differentiation into osteoblasts. The optimum conditions were found to be a mixture of gelatin and agarose for the coating in the cartilage phase and low mineralized collagen content for the bone phase.