The search for biomaterials and techniques that minimize the number of surgical interventions and that provide efficient bone repair without the presence of microorganisms is necessary mainly in intraoral bone grafting procedures. Therefore, this study aimed to develop nanofibrous hydrogels that facilitate the repair of a bone defect with simultaneous local decontamination. The proposed biomaterial has a type-B gelatin base associated with β-type tricalcium phosphate (β-TCP) and methylene blue (MB), which is a photosensitizer used in antimicrobial photodynamic therapy (aPDT). Nanofibrous hydrogels made of pure gelatin, hydrogels of gelatin with β-TCP, hydrogels of gelatin with MB or hydrogels of gelatin with β-TCP and MB were prepared and obtained by electrospinning using a rotating collector. The incorporation of MB at 0.05% (w/v, aqueous solution) was carried out by swelling the sample in this solution. The characterization of the hydrogels was carried out by scanning electron microscopy (SEM), swelling test, Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). Stable nanofibrous hydrogels were produced, with uniform distribution of β-TCP. Biomaterials containing MB were uniformly blue in color. The incorporation of MB and β-TCP does not interfere with the thermal degradation of the developed biomaterials. It is concluded that the biomaterials developed in this study are promising for future clinical application, and may be viable in therapies that require simultaneous tissue repair and decontamination.