Magnetron sputtering is a well-established fabrication technique in industry for the deposition of transparent conductive oxides toward optoelectronic device applications. However, the bombardment with highly energetic O^- ions can damage underlying sensitive layers of devices or the growing film itself, being a critical issue. Its substrate-dependent impact is not fully understood. Herein, the early-stage dynamics of film growth and ion-bombardment-induced degradation are studied independently by applying two distinct templates as substrates for indium zinc oxide (IZO) deposition via radio frequency magnetron sputtering, with real-time monitoring via in situ grazing-incidence small-angle X-ray scattering (GISAXS). X-ray reflectivity results reveal that O- ion-bombardment results in a reduced density and modified surface morphology of spin-coated ZnO nanoparticle (NP) films, despite a relatively high working pressure, whereas commercially sputter-coated polycrystalline indium tin oxide (ITO) films exhibit stronger resistance, enabling the successful formation of an IZO layer. Quantitative analysis of GISAXS data shows that the growth regimes of IZO deposited on the ITO film undergo the stages of nucleation, adsorption-driven coalescence, and layer formation. Conversely, the degradation dynamics on the ZnO NP film exhibit a cyclical pattern under ion bombardment, characterized by alternating phases of adsorption-desorption equilibrium, physical degradation, reestablished adsorption-desorption equilibrium, and surface amorphization.