Given the important aspects of wound healing approaches, in this work, an innovative biocompatible nanobiocomposite scaffold was designed and prepared based on cross-linked lignin–agarose hydrogel, extracted silk fibroin solution, and zinc chromite (ZnCr2O4) nanoparticles. Considering the cell viability technique, red blood cell hemolysis in addition to anti-biofilm assays, it was determined that after three days, the toxicity of the cross-linked lignin–agarose/SF/ZnCr2O4 nanobiocomposite was less than 13%. Moreover, the small hemolytic effect (1.67%) and high level of prevention in forming a P. aeruginosa biofilm with low OD value (0.18) showed signs of considerable hemocompatibility and antibacterial activity. Besides, according to an in vivo assay study, the wounds of mice treated with the cross-linked lignin–agarose/SF/ZnCr2O4 nanobiocomposite scaffold were almost completely healed in five days. Aside from these biological tests, the structural features were evaluated by FT-IR, EDX, FE-SEM, and TG analyses, as well as swelling ratio, rheological, and compressive mechanical study tests. Additionally, it was concluded that adding silk fibroin and ZnCr2O4 nanoparticles could enhance the mechanical tensile properties of cross-linked lignin–agarose hydrogel, and also an elastic network was characterized for this designed nanobiocomposite.