We report a multi-modal study of the electrical, chemical and structural properties of a kesterite thin-film solar cell by combining the spatially-resolved X-ray beam induced current and fluorescence imaging techniques for the evaluation of a fully functional device on a cross-section. The data allowed the correlation of the chemical composition, defects at interfaces and inhomogeneous deposition of the layers with the local charge-collection efficiency of the device. We support our observations with Monte Carlo simulations of high-energy X-ray interactions with the semiconductor device, and finite-volume modeling of the charge-collection efficiency.