A green way is introduced to biosynthesis of ZnO@TiO2@SiO2 and Fe3O4@SiO2 nanocomposites using the bioactive potential of Lecanora muralis (LM) lichen. UV‐Vis spectroscopy and GC–Mass analysis of the lichen show the presence of various bioactive constituents inside the lichen aqueous extract. The XRD, SEM, EDS, and elemental mapping techniques revealed the well fabrication of biosynthesized nanostructures. Also, investigation of antibacterial and antifungal activities of nanostructures demonstrated that green synthesized nanostructures have a very good antibacterial ability against Staphylococcus aureus, Escherichia coli, Pseudomonas spp. and Candida spp. pathogenic bacteria, and fungi but no antifungal activity toward the Aspergillus flavus, Aspergillus niger, and Aspergillus terrus fungi species. This study investigates the greener pathway toward the synthesis of lichen‐based ZnO@TiO2@SiO2 and Fe3O4@SiO2 nanocomposites and investigation of their biological activities.