Growth of amorphous SiO2 thin films deposited by reactive magnetron sputtering at low temperatures has been studied under different oxygen partial pressure conditions. Film microstructures varied from coalescent vertical column-like to homogeneous compact microstructures, possessing all similar refractive indexes. A discussion on the process responsible for the different microstructures is carried out focusing on the influence of (i) the surface shadowing mechanism, (ii) the positive ion impingement on the film, and (iii) the negative ion impingement. We conclude that only the trend followed by the latter and, in particular, the impingement of O- ions with kinetic energies between 20 and 200 eV, agrees with the resulting microstructural changes. Overall, it is also demonstrated that there are two main microstructuring regimes in the growth of amorphous SiO2 thin films by magnetron sputtering at low temperatures, controlled by the amount of O2 in the deposition reactor, which stem from the competition between surface shadowing and ion-induced adatom surface mobility.