Room temperature focused electron beam (FEB) induced deposition of contamination‐free transparent materials is a major issue for the FEB production of nano‐optical structures, microchip editing (insulating and passivation layers), and photolithography mask repair. In this work, stoichiometric SiO2 is successfully deposited from three different organosilanes: tetraethoxysilane (TEOS, Si(OCH2CH3)4), tetramethoxysilane (TMOS, Si(OCH3)4), and tetramethylsilane (TMS, Si(CH3)4). The FEB depositions are assisted by a molecular oxygen flux injected simultaneously with the precursor gas. The dependencies on the additional oxygen flux of the chemical compositions of the resulting deposits are studied in detail. Threshold [O2]:[precursor] molecular flux ratios, above which carbon is no longer detectable in the deposited material, are 1.75, 0.15, and 0.05, for TEOS, TMOS, and TMS, respectively. Contamination side‐reactions such as oxygen incorporation in the deposited material due to residual gases in the scanning electron microscope (SEM) chamber are shown to be significant at standard high‐vacuum operating pressures of 5 × 10–5 mbar. The quality of deposited SiO2 obtained from the three precursors is estimated by exposing the material to standard industry cleaning procedures. The etching tests indicate that TMS leads to denser deposits than the two other silanes. The optical transmissions of the deposited SiO2 obtained from TMOS and TMS are measured at 193 nm wavelength, and are 80 % and 99 %, respectively. The latter value fulfills the photomask repair requirements. Finally, hypothetical decomposition pathways of the various silanes used are discussed.