A method was developed to determine the modal mineralogy and Sn deportment of a fine-grained skarn ore. Mineral Liberation Analysis (MLA) and electron probe microanalysis were applied to crushed and uncrushed samples for mineralogical characterization. A comprehensive list of mineral references consisting of energy dispersive X-ray spectra and information about elemental concentration and density was created. This conventional approach did not achieve reliable results in the characterization of some of the analyzed ore types. Small grain sizes and the variety of Sn-bearing minerals required adding mineral references with manually mixed EDX-spectra, calculated elemental concentrations and densities. Comparison of MLA data using this modified approach with bulk geochemistry and X-ray powder diffraction illustrates very good agreement for all ore-types characterized. The new approach may well be considered for other mineralogically complex ores containing, a multitude of ore minerals and complex deportment of metals.