Lignin, being a natural antioxidant and antimicrobial underutilized biopolymer derived mainly from agro-waste, is a material of great interest. In this study, lignin was chosen as a matrix to synthesize silver–gold bimetallic and monometallic nanocomplexes to explore the synergistic antioxidant and antimicrobial properties of the lignin stabilized nanoagents. The synthesis of the nanocomplexes was carried out using a one pot method, utilizing lignin as the sole source for reducing, capping, and stabilizing the nanoagents. Further, characterization studies were performed to determine the exact structure of the nanocomplexes. The developed nanocomplexes were found to possess substantial phenolic and flavonoid contents, which contributed to their high antioxidant activity. Further, the antioxidant and antimicrobial activity of the lignin–bimetallic and monometallic nanocomplexes was evaluated and compared with pristine lignin. Moreover, the mechanism behind the antimicrobial activity of the nanocomplexes was elucidated through various methods, namely, reactive oxygen generation, nucleic acid leakage, and DNA cleavage studies. The obtained results were greatly supported by scanning electron microscopy, transmission electron microscopy, and live–dead cell imaging techniques. This study is a contribution in converting waste to value added functional nanomaterials for potential antioxidant and antimicrobial applications.