In this work reports the synthesis of iron oxide along with the complex formation from the neem cake using the biosynthesis and precipitation method. Ferrous sulphate (FeSO4) and sodium hydroxide were used as the precursor precipitating agent, respectively. The resultant specimens were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), ultra-violet visible spectroscopy (UV-Vis), fourier-transform infrared spectroscopy (FT-IR), soil test, biochemical, and phytochemical analysis. To test the effect of the synthesized specimen as the nanofertilizer in the seed germination and the growth, the sample was incorporated in to the red soil and the agronomical traits including plant height. Number of leaves were studied over a survival period of 75 days of the selected plant species vigna mungo using POT analysis. The plant samples were harvested, and then the biochemical and phytochemical studies were carried out for alkaloids, glycosides, flavonoids, phenols, steroids, protein and total chlorophyll content. The results showed that the nanoparticles incorporation enhanced the plant growth and increased the concentration of the bioactive compounds in an appreciable level.