Pyrrhotite exhibits diverse non-stoichiometric superstructures with varied surface reactivities, causing contradictory flotation behaviors in industrial processes. The challenges in managing pyrrhotite in processing plants stem from the lack of systematic mineralogical techniques to distinguish its superstructures in low-grade ore samples without any preprocessing, such as purification or manual sample picking. This study established a comprehensive technique to differentiate between pyrrhotite superstructures in low-grade metal sulfide ores using spectroscopic and microscopic methods. The examined samples came from a natural copper–gold orebody from Western Australia and the flotation concentrate of the ore. Initial identification of pyrrhotite through XRD confirmed the presence of pyrrhotite in the samples but failed to discern magnetic and nonmagnetic pyrrhotite superstructures due to the samples' low pyrrhotite content and XRD peak overlaps. In this regard, magnetic colloid technique (MCT) was utilized to effectively identify the presence of both magnetic and nonmagnetic pyrrhotite superstructures in the samples. Energy-dispersive X-ray spectroscopy (EDS) analysis revealed the Fe:S (at.%) ratio ranging from 0.840 to 0.930 for both the ore and the flotation concentrate, affirming the presence of both magnetic and nonmagnetic pyrrhotite with possible 4C, 5C and 6C superstructures. Based on the information obtained from XRD, MCT and EDS, Electron Backscatter Diffraction (EBSD) analysis successfully solved the challenge of identifying pyrrhotite superstructures. By comparing Kikuchi patterns from various zones with different Fe:S ratios to reference patterns, the EBSD confirmed the presence of 4C, 5C and 6C pyrrhotite superstructures in the examined samples. This methodology establishes a comprehensive framework for identifying pyrrhotite superstructures in complex ore samples, offering insights for industrial applications.