Multiphoton lithography, based on multiphoton polymerization, is a powerful technique for the fabrication of complex three-dimensional (3D) structures. Herein, we report on the photostructuring of novel biopolymer-based hybrid hydrogels, comprising gelatin methacrylamide and a water-soluble chitosan derivative, via multiphoton polymerization. The nontoxic, Food and Drug Administration-approved, biocompatible photosensitizer eosin Y was exploited as the sole photoinitiator, without the coinitiators and/or comonomer that are commonly used, allowing for further expansion of the available wavelengths up to 800 nm. Importantly, the obtained hybrid material exhibits excellent biocompatibility, evidenced by the increased proliferation of dental pulp stem cells, compared with the individual components and the polystyrene control, after 7 days in culture. Additionally, the 3D hybrid scaffolds promote the matrix mineralization, following their functionalization with bone morphogenetic protein 2. These tailor-made synthetic, biocompatible materials pave the way for further opportunities in 3D scaffold fabrication, including in situ and in vivo biofabrication.