This study evaluates the applicability of the clumped isotope thermometry to mesothermal hydrothermal systems (5–10 km depth; 250–450 °C). We measured Δ₄₇, δ¹⁸O and δ¹³C of calcite as well as δ¹⁸O of cogenetic minerals from typical quartz-calcite ± tourmaline±chlorite orogenic veins from the Neoarchean Augmitto-Bouzan orogenic gold deposits (Abitibi, Canada). Our findings show that caution is required when utilizing the clumped isotope thermometry in the study of old mesothermal deposits. Temperatures calculated from Δ₄₇ values are systematically and significantly shifted to low temperature, i.e., ∼150 °C rather than the ∼350 ± 50 °C expected for orogenic gold deposit formation and documented using oxygen isotope equilibrium between mineral pairs. We show that the low temperatures estimates resulted from solid-state reordering that occurred in calcite grains during the cooling history of the vein-hosting rocks. Because the fast cooling rates required to preserve the initial temperature of calcite formation in mesothermal hydrothermal systems are geologically unrealistic, we suggest that refractory minerals (i.e., minerals with higher blocking temperature such as magnesite, dolomite, ankerite) should be investigated to apply clumped isotope thermometry in such context.