The effectiveness of this methodology is illustrated with a study of the Acoculco Caldera, which is a geothermal prospective area. Two major alteration zones have been recognized: a shallow one with ammonium illite, and a deeper one with epidote–calcite–chlorite. Four additional mineral assemblages have been identified: (a) buddingtonite and (b) smectite, in the recent volcanic sequence, and (c) calcite marble and (d) granitic rocks, in the Mesozoic basement. The shallow alteration zone extends to a depth of 500–600 m, affecting most of the caldera sequence. It consists of a pervasive ammonium-argillic alteration of ignimbrites and dacitic lavas. Although ammonium illite is the main alteration mineral, kaolinite (sensu lato), buddingtonite and smectite locally occur at depths down to 300 m. The occurrence of ammonium silicates suggests temperatures above 200 °C. There is a positive correspondence between the abundance of ammonium minerals and the total nitrogen content of the rocks. The highest value (0.65 N wt. % ) corresponds to a sample rich in buddingtonite. Ammonia is probably derived from the organic matter in the Mesozoic sedimentary series underlying the caldera.