Iron oxide (Fe3O4) nanoparticles (NPs) were synthesized by co-precipitation method, further Fe3O4-NPs was encapsulated under inert environment with poly-indole carboxylic acid, finally the product obtained as poly-indole carboxylate iron oxide nanoparticles(PIFe3O4-NPs). Then, the both products Fe3O4-NPs and PIFe3O4-NPs were characterized and confirmed the composition of elements using X-ray diffraction pattern (XRD). The change in shape and morphology of products was confirmed by scanning electron microscopy (SEM). The functional groups and shifting of vibrational bands due to the coordination of both Fe3O4 and ligand are studied using Fourier transform infrared (FT-IR) spectra. The band gap of the products were measured using Ultraviolet–visible (UV–Vis.) spectra and also measured the direct and indirect band gap using Tauc plot. To investigate the binding nature of the sample, a molecular docking study was carried out and the results indicated that the PIFe3O4 moiety formed five hydrogen bonds with amino acid residues of Aspergillus niger ATCC9642 isopullulanase (2Z8G). The oxygen atom of Fe3O4-NPs binds well with the active sites of Staphylococcus Aureus Protein A (1BDC) and Escherichia Coli thioredoxin reductase (1TDE) with the ASN24, GLY17, ALA16, GLY14, and GLY113 residual interactions. Therefore, the results of molecular docking emphasized that the target Fe3O4-NPs nanoparticles can bind more easily to the target proteins 1BDC, 1TDE, and 2Z8G. In addition to that, antioxidant, antibacterial and antifungal activities were also examined. These findings demonstrate that PIFe3O4-NPs have antimicrobial and antioxidant properties and therefore it confirms the use of PIFe3O4-NPs in the treatment of infection against fungus, gram-positive and gram-negative bacteria.