techniques including room and cryogenic temperature atomic scale high-resolution and scanning transmission electron microscopy (HR-TEM and STEM), atomic force microscopy (AFM), and the time-of-flight secondary ion mass spectroscopy (TOF-SIMS) to reveal the existence of the niobium hydride precipitates directly in the Rigetti chip areas. Electron diffraction and high-resolution transmission electron microscopy (HR-TEM) analyses are performed at room and cryogenic temperatures (~106 K) on superconducting qubit niobium film areas, and reveal the formation of three types of Nb hydride domains with different crystalline orientations and atomic structures. There is also variation in their size and morphology from small (~5 nm) irregular shape domains within the Nb grains to large (~10-100 nm) Nb grains fully converted to niobium hydride. As niobium hydrides are non-superconducting and can easily change in size and location upon different cooldowns to cryogenic temperatures, our findings highlight a new previously unknown source of decoherence in superconducting qubits, contributing to both quasiparticle and two-level system (TLS) losses, and offering a potential explanation for qubit performance changes upon cooldowns. A pathway to mitigate the formation of the Nb hydrides for superconducting qubit applications is also discussed.