We report on the analysis of stress-induced structural changes and the formation of an omega $\left(\omega \right)$ phase in polycrystalline Nb thin films deposited on Si by high-power impulse magnetron sputtering (HiPIMS) for superconducting qubits using x-ray diffraction (XRD), transmission electron microscopy (TEM), and density-functional theory (DFT). XRD analysis indicates that internal stresses in the Nb thin films lead to the formation of $\left\{112\right\}\langle 111\rangle$ deformation twins and TEM analysis shows that $\omega$ phases nucleate at some of the twin boundaries in the Nb thin films. The size of $\omega$ phases ranges from 10 to 100 nm, which is comparable to the coherence length of Nb $(\approx 40 \mathrm{nm})$, and $\approx 1\%$ volume fraction of Nb grains exhibit this $\omega$ phase. The details of the formation mechanism and superconducting properties of the $\omega$ phases are investigated by DFT and potential roles of the $\omega$ phase in Nb as a source of decoherence in superconducting qubits are also discussed.

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• Defects
• Microstructure
• Phase transitions
• Structural properties
• Superconductivity