AbstractUnderstanding the mechanisms that connect heat and electron transport with crystal structures and defect chemistry is fundamental to develop materials with thermoelectric properties. In this work, we synthesized a series of self‐doped compounds Cu2+xMn1−xGeS4 through Cu for Mn substitution. Using a combination of powder X‐ray diffraction, high resolution transmission electron microscopy and precession‐assisted electron diffraction tomography, we evidence that the materials are composed of interconnected enargite‐ and stannite‐type structures, via the formation of nanodomains with a high density of coherent interfaces. By combining experiments with ab initio electron and phonon calculations, we discuss the structure–thermoelectric properties relationships and clarify the interesting crystal chemistry in this system. We demonstrate that excess Cu+ substituted for Mn2+ dopes holes into the top of the valence band, leading to a remarkable enhancement of the power factor and figure of merit ZT.