Biosilica obtained from frustules of diatoms have very delicate nanostructures similar to many micro- and nanofluidic devices. In the present investigation, a cheaper and ecofriendly metal-oxide-semiconductor (MOS) tool has been fabricated exploiting frustules of the diatom Halamphora subturgida. The structural, optical, and chemical characterizations of the cleaned frustules of cultured diatom were investigated through various techniques. Electron microscopic images revealed intricate morphology of the nanostructured silica with very minute pores making the frustules very hard but light material. UV-Vis spectroscopy showed maximum absorbance at 223 nm. The absorption maximum for photoluminescence was centered at 462 nm and that of cathodoluminescence was at 439.9 nm and 466.6 nm. Bulk of extracted silicon dioxide (SiO2) nano-powder from diatom frustules was used as a source material for preparing a high-quality crystalline film on P-type silicon (p-Si) by vapor-liquid-solid (VLS) method. The crystalline quality of the film was tested by X-ray diffraction (XRD) and the crystalline size obtained was 62 ± 2.4 nm. From scanning electron microscopic (SEM) investigation, the growth of a continuous film from diatom biosilica on p-Si substrate was revealed. The thickness of the as-grown SiO2 film was 22.2 ± 1.6 nm, obtained from spectroscopic ellipsometry (SE) study. The performances of fabricated Al/SiO2/Si metal-oxide-semiconductor capacitor were tested by measuring leakage current (~ 43 ± 8 × 10−11 A μm−2 at +2 V), capacitance-voltage, constant current (0.1 μA), and voltage stress (at − 2 V) for reliable gate dielectrics applications in MOS devices. Overall, the process was cost-effective and provides an alternative technique to design high-quality diatom-derived “Bio-SiO2 films” on p-Si substrate. [Figure not available: see fulltext.]. © 2020, Springer Nature B.V.