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Samples from the opus sectile panel excavated from the Episcopal Residence building at the archaeological site of Stobi were examined using X-ray powder diffraction, SEM-EDS, and Raman spectroscopy. The analyzed samples, exhibiting plentiful color and surface variations, comprise the reconstructed sectile panel as well as represent the in situ ground remains. The complementary techniques revealed dominant amorphous phase in five samples, whereas the remaining seven specimens confirmed the presence of magnesite, quartz, dolomite, ankerite, cuprite, wüstite, and hematite. The work represents the first systematic attempt to determine the mineral phases in the restored opus sectile panel, assembled by decorative minerals forming a geometric net of polychrome crosses. Furthermore, the mineral characterization has revealed an origin of mineral species not typical for Macedonian terrain (ankerite, wüstite, cuprite, transparent quartz) that lead to the conclusion that the samples were likely imported from other early-Christian communities.