The aim of this study is to design a therapeutic enhanced threedimensional (3D) silk fibroin (SF)-based scaffold containing propolis (Ps)-loaded chitosan (CH) nanocarriers. To this aim, we initially synthesized a hybrid gel-based ink by a synergistic sol−gel and self-assembly approach and then processed the resulting gels by microextrusion-based 3D printing followed by supercritical drying to obtain 3D hybrid aerogel scaffolds. Ps was utilized to enhance the final scaffold's bactericidal efficacy and cell responsiveness. For the synthesis of the scaffold, two Ps loading methods (in preprint and postprinting steps) were investigated in order to optimize the Ps drug quantities in the scaffold and maximize the antibacterial properties of scaffold. In the postprinting Ps loading step, the hybrid silica−oxidized SF (SFO)−CH hydrogel ink was 3D printed into a construct with an interconnected porous structure, and then, Ps was loaded into the printed construct. In the preprint loading method, PS was incorporated into the SF and a hydrolyzed silane solution prior to gelation. The morphological studies demonstrate that the addition of Ps encapsulated CH nanoparticles (NPs) into the hydrogel solution improved the porosity of the developed scaffolds. The rheological analysis of the designed gel ink with and without Ps loading and the release kinetics were studied. The antimicrobial results show that the Ps-loaded scaffolds in the postprinting step exhibited superior antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) strains compared to a preprinted Ps-loaded scaffold. Direct and indirect in vitro cytotoxicity tests also confirmed the designed Ps-loaded scaffold biocompatibility toward a mouse fibroblast (L929) cell line. We demonstrated that the scaffold formulated by propolis-loaded chitosan NPs can enhance the migration and proliferation of L929 fibroblast cells. The obtained results prove the promise of the designed 3D printed silica−SFO−CH−Ps scaffolds as a potent 3D scaffold to mediate tissue regeneration but also as an antibacterial highly porous matrix to support wound healing.