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Direct analysis of matrix and admixture elements in non-conducting crystals is a relevant analytical task in terms of quality assurance of optical materials. The current study aimed to develop a method capable to assess the inhomogeneity of optical crystals with sufficient sensitivity. K1−xRbxTiOPO4 (x = 0.002 and 0.05) and KGd1−yNdy(WO4)2 (y = 0.05) were grown using the top-seeded solution growth method (TSSG). The samples were analyzed by microsecond direct current pulsed glow discharge time-of-flight mass spectrometry (µs-PDC TOF GDMS). The data were compared with the results obtained by scanning electron microscope-energy dispersive X-ray spectroscopy (SEM EDX) and spectrophotometry and validated by the analysis of certified reference material. Sample glow discharge sputtering and analysis were optimized and implemented in real samples. Sample coating with a silver layer and sample pressing in the metallic matrix were proposed to ensure effective sputtering for K1−xRbxTiOPO4 and KGd1−yNdy(WO4)2, respectively. Using the designed method, the inhomogeneity of the dopant’s distribution was demonstrated along the growth axis and in the case of K1−xRbxTiOPO4, also in the growth sectors of different faces. The designed method is applicable for the direct analysis of optical crystal and may be implemented in quality assurance in the manufacturing of optical materials.