Green chemistry approach was employed to synthesize Silica nanoparticles (SiNPs) using aqueous extract of Bryophyllum pinnatum leaf as capping agents. The physicochemical properties of formed nanoparticles were successfully completed through sophisticated characterization methods such as UV-Visible absorbance spectroscopy, Fourier Transform Infra-Red spectroscopy, X-Ray Diffraction, Scanning Electron Microscope, Energy Dispersive X-Ray, Zeta Potential Analysis and Thermo-Gravimetric Analysis. All the characterization results were indicating that the spherical morphology, amorphous nature with an average size of 24 nm of nanoparticles formed. FT-IR results highlighted the key bioactive compounds that could be responsible for capping and reduction to formation of SiNPs. As synthesized SiNPs shows excellent stability with negative zeta potential value − 32 mV. The biomolecules from B. pinnatum were successfully working for the formation of SiNPs with spherical shape. Moreover, to assess agricultural application of green synthesized SiNPs was carried out by seed germination assay on Vigna radiata. The seed germination assay confirms that the low concentration of SiNPs enhances the seed germination. Meanwhile, the higher concentration of the SiNPs inhibits the seed germination, shoot and root formation. SiNPs at optimum concentration could be used in the agriculture field as nano growth promoters.