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Abstract Understanding crystal characteristics down to the atomistic level increasingly emerges as a crucial insight for creating solid state platforms for qubits with reproducible and homogeneous properties. Here, isotope concentration depth profiles in a SiGe/28Si/SiGe heterostructure are analyzed with atom probe tomography (APT) and time‐of‐flight secondary‐ion mass spectrometry down to their respective limits of isotope concentrations and depth resolution. Spin‐echo dephasing times T2echo=128μs and valley energy splittings EVS around 200μeV have been observed for single spin qubits in this quantum well (QW) heterostructure, pointing toward the suppression of qubit decoherence through hyperfine interaction with crystal host nuclear spins or via scattering between valley states. The concentration of nuclear spin‐carrying 29Si is 50 ± 20ppm in the 28Si QW. The resolution limits of APT allow to uncover that both the SiGe/28Si and the 28Si/SiGe interfaces of the QW are shaped by epitaxial growth front segregation signatures on a few monolayer scale. A subsequent thermal treatment, representative of the thermal budget experienced by the heterostructure during qubit device processing, broadens the top SiGe/28Si QW interface by about two monolayers, while the width of the bottom 28Si/SiGe interface remains unchanged. Using a tight‐binding model including SiGe alloy disorder, these experimental results suggest that the combination of the slightly thermally broadened top interface and of a minimal Ge concentration of 0.3% in the QW, resulting from segregation, is instrumental for the observed large EVS=200μeV. Minimal Ge additions