Pyrrole-2-carboxylic acid functionalized Fe3O4 nanoparticles as a novel organic–inorganic hybrid heterogeneous catalyst was manufactured and characterized by X-ray diffraction (XRD) analysis, Fourier transform infrared (FT-IR), Transmission Electron Microscopy (TEM), Thermogravimetric analysis (TGA), Scanning electron microscope (SEM), Vibrating sample magnetometer (VSM) techniques. The catalytic activity of the nanomagnetic catalyst was investigated in the new heterocyclic system isoxazolo[4,3-e]indazole was synthesized via the nucleophilic substitution of a hydrogen in 5-nitro-1-p-tolyl-1H-indazole with different 2-phenylacetonitrile derivatives in basic medium. The synthetic compounds exert moderate activity against both Gram positive and Gram negative bacteria and their effectiveness is higher against Bacillus subtilis. This green magnetic nanocatalytic procedure has a good reversibility and provides clean production in a short reaction time.