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We investigated the correlation between the surface finish and luminescence properties of chemically polished cerium-doped single-crystal Gd3Al2Ga3O12 scintillators (Ce:GAGG), from the crystallographic perspective. The intrinsic defects in the crystals were identified via photoluminescence spectroscopy followed by scanning electron microscopy and X-ray diffraction to analyze their surface morphologies. Finally, the samples were individually wrapped with an enhanced specular reflector (ESR), coupled with a photomultiplier tube, placed inside a dark box, connected to a digitizer, and irradiated with a 137Cs radioactive source to evaluate the relative light (signal) output and energy resolution of each sample. The as-cut (rough) Ce:GAGG single-crystal samples, that were chemically polished with phosphoric acid at 190°C in air for 60 min, demonstrated a 33.1% increase in signal amplitude (light output to photosensor) and 2.4% (absolute value) improvement in energy resolution, which were comparable to those obtained for the mechanically polished sample. For these samples, the surface roughness was found to be ~430 nm, which was approximately half of that of the mechanically polished sample. The chemical polishing method used in this study is a cost-effective and straightforward technique to improve structural imperfections and can facilitate the treatment of inorganic scintillators with complex shapes and/or on a large scale.