Spherical submicrometer-sized silica particles were prepared from a reaction mixture containing tetraethoxysilane, ammonia and ethanol, and deposited onto silicon wafers. The properties of these SiO2 particles depend on their size, size distribution and shape. Even if some of these characteristics can be perfectly controlled by appropriate synthesis conditions, several alternative approaches must be explored in order to modify the shape of silica particles. The samples were then irradiated at room temperature with Si ions at different energies (4, 6 and 8 MeV) and fluences up to 5×1015 Si/cm2, at an angle of 45° with respect to the sample surface. After the Si irradiation the spherical silica particles turned into ellipsoidal particles, as a result of the increase of the particle dimension perpendicular to the ion beam and a decrease in the parallel direction. This effect increases with the ion fluence and depends on the electronic energy loss of the impinging ions. We observed that the particle deformation decreases with the beam energy, mainly because our samples were irradiated at room temperature. Thermal effects must be studied in detail in order to elucidate the complete deformation mechanism, as the existence of additional mechanisms related to the electronic energy loss effects can not be excluded.