The Cu₂ZnSnS₄ kesterite is currently among the most promising inorganic, nontoxic, earth-abundant materials for a new generation of solar cells. Interfacial defects and secondary phases present in the kesterite active layer are, however, detrimental to the performance of the device. They are typically probed with techniques that are destructive or limited to the surface, and x-ray diffraction cannot reliably distinguish small amounts of zinc sulfide or copper tin sulfide from kesterite. Conversely, resonant ptychographic tomography, which relies on electron density contrast, overcomes these limitations. Here, we demonstrate how this technique can enable localization and quantification of secondary phases, along with measurements of adherence at the interfacial layers, on complete and functioning devices. In our experiment, we utilize an x-ray energy value far from absorption edges as well as three single energies corresponding to the absorption edges of Cu, Zn, and Sn, to gain elemental sensitivity to these elements and enhance contrast between phases with similar electron density. As a result, we image and identify in the active layer grains of a secondary phase, namely, zinc sulfide, which is not easily discriminated by other standard characterization techniques. In addition, we are able to observe Cu diffused from the active layer into the CdS buffer layer as well as Cu in the form of copper sulfide at their interface. Other relevant morphological features are best resolved off-resonance at the optimal energy for the synchrotron beamline with ∼20 nm resolution.