The majority of the ∼100 Holocene calderas on Earth host vigorously active hydrothermal systems, the heat and volatile budgets of which are sustained by degassing of deeply stored magma. Calderas may thus contribute a nontrivial, although poorly quantified, fraction of the global budget of magmatic volatiles such as CO2. Here we use original isotopic and petrological results from Campi Flegrei volcano, Italy, to propose that hydrothermal calcites are natural mineral archives for the magmatic CO2 that reacted with reservoir rocks during the geological history of a caldera. We show that Campi Flegrei calcites, identified in core samples extracted from 3-km-deep geothermal wells, formed at isotopic equilibrium with magmatic fluids having δ18OH2O of +8.7‰ to +12.7‰, and δ13CCO2 of ∼−1.5‰. This inferred fossil fluid composition is virtually identical to that of present-day fumaroles, demonstrating a stable carbon source during the caldera’s (<40 k.y.) history. We use the mass of calcites stored in the hydrothermal system to estimate that 12 Gt of magmatic CO2 reacted with the Campi Flegrei rocks during the caldera history; this corresponds to a time-averaged CO2 flux of ∼800 t d–1. This long-term CO2 flux, the first of its kind in the geological literature, is similar to the present-day soil CO2 degassing flux (1100 ± 200 t d–1). We conclude that the actual magmatic CO2 degassing flux from calderas may be severely underestimated if subsurface calcite precipitation is not taken into account.