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The presence of inclusions, twinning, and low-angle grain boundaries, demanded to exist by the third law of thermodynamics, drive the behavior of quantum materials. Identification and quantification of these structural complexities often requires destructive techniques. X-ray micro-computed tomography (µCT) uses high-energy X-rays to non-destructively generate 3D representations of a material with micron/nanometer precision, taking advantage of various contrast mechanisms to enable the quantification of the types and number of inhomogeneities. We present case studies of µCT informing materials design of electronic and quantum materials, and the benefits to characterizing inclusions, twinning, and low-angle grain boundaries as well as optimizing crystal growth processes. We discuss recent improvements in µCT instrumentation that enable elemental analysis and orientation to be obtained on crystalline samples. The benefits of µCT as a non-destructive tool to analyze bulk samples should encourage the community to adapt this technology into everyday use for quantum materials discovery.