Pyrrhotite, a significant sulfide mineral in base metal sulfide deposits, exists in various superstructures including magnetic (4C) and non-magnetic (5C and 6C) types. Identifying and quantifying pyrrhotite superstructures in an ore sample has been a challenge, hindering efforts to improve pyrrhotite rejection in copper–gold flotation. This study employed synchrotron X-ray powder diffraction (S-XRPD) analysis to quantify pyrrhotite superstructures in the concentrates obtained from flotation of a copper–gold ore after grinding with forged steel and 30% chromium grinding media. S-XRPD demonstrated a superior capability in detecting characteristic peaks of 4C, 5C and 6C pyrrhotite superstructures compared to conventional XRPD. Utilizing the Rietveld refinement method, the identified pyrrhotite superstructures were quantified. These findings were successfully validated through independent X-ray fluorescence analysis on elemental compositions. The quantification work demonstrated that 30% chromium grinding media enhanced the floatability of all pyrrhotite superstructures over forged steel grinding media and each pyrrhotite superstructure in the copper–gold ore resembled a copper sulfide mineral rather than pyrite in response to grinding media during flotation. This research highlights the potential of S-XRPD as an effective technique for identifying and quantifying pyrrhotite superstructures in ore samples and determining their flotation behaviors.