Superconducting quantum devices, typically operating at millikelvin temperatures, rely on materials whose nanoscale defects significantly impact coherence times. While transmission electron microscopy (TEM) is a powerful tool for characterizing these defects, such as surface oxides on Nb and Ta, most analyses are performed at room temperature (RT). This raises two critical questions: (1) Does the electronic structure of these oxides remain stable at cryogenic temperatures, validating RT analysis? (2) Can cryogenic conditions mitigate the electron beam damage often observed in insulating substrates like sapphire? In this study, we employed in-situ cryogenic scanning TEM (Cryo-STEM) and electron energy-loss spectroscopy (EELS) to investigate Nb or Ta oxides and sapphire substrates at RT, liquid nitrogen (LN2), and liquid helium (LHe) temperatures. We demonstrate that the electronic structures of amorphous Nb2O5 and Ta2O5 remain virtually unchanged from RT down to LHe, confirming that RT-acquired data can provide meaningful insights for interpreting low-temperature device performance. By systematically tracking the O K-edge fine structures and transition metal edges, we confirmed the preservation of intrinsic oxidation states and crystal-field splitting without beam-induced reduction. Our study validates the reliability of standard RT characterization for assessing the electronic structure of oxides. Furthermore, by utilizing Energy-Filtered imaging and Al L-edge fine structure analysis to directly visualize the damage pathways, we report that cooling to cryogenic temperatures effectively suppresses beam-induced structural damage and preserves the medium-range ordering of the sapphire substrates, even under high probe currents (200 pA). These findings confirm Cryo-STEM as a robust benchmarking methodology for high-fidelity characterization of materials in quantum devices.