The quantitative phase analysis using X-ray diffraction of pyrite ore concentrate samples extracted from the Thackaringa mine is problematic due to poor particle statistics, microabsorption and preferred orientation. The influence of sample preparation on these issues has been evaluated, with ball milling of the powder found most suitable for accurate and precise quantitative phase analysis. The milling duration and other aspects of sample preparation have been explored, resulting in accurate phase reflection intensities when particle sizes are below 5 µm. Quantitative phase analysis on those samples yielded precise phase fractions with standard deviations below 0.3 wt%. Some discrepancy between the elemental composition obtained using X-ray powder diffraction data and that determined using wavelength-dispersive X-ray fluorescence was found, and is thought to arise from unaccounted for crystalline phase substitution and the possible presence of an amorphous phase. This study provides a methodology for the precise and accurate quantitative phase analysis of X-ray powder diffraction data of pyrite ore concentrate from the Thackaringa mine and a discussion of the limitations of the method. The optimization process reveals the importance of confirming reproducibility on new samples, with as much prior knowledge as possible.