The Organ cauldron and its underlying plutonic roots are exposed through a vertical section 5–6 km thick in the Organ Mountains of south central New Mexico. Emplaced within a 1 m.y. time span at 33.7–32.8 Ma, both cauldron fill tuffs and lavas, as well as the underlying Organ batholith, document emplacement of a chemically and mineralogically zoned magma chamber at shallow depths. The tuffs, as much as 3.0 km thick near the center of the cauldron, show rather simple normal chemical and mineralogical gradients which indicate zoning in the magma chamber from aphyric rhyolite (77% SiO 2 ) at the top to crystal‐rich rhyolite (68% SiO 2 ) at deeper levels. Lava flows, more than 0.3 km thick, overlie the tuffs and apparently represent still deeper, more mafic (68–61% SiO 2 ), crystal‐rich parts of the erupted magma volume. The oldest phase of the batholith may also be compositionally zoned from quartz syenite (68% SiO 2 ) at the top to monzodiorite (55% SiO 2 ) at the lowest exposed level. This phase of the batholith, which forms both a concordant floor beneath the volcanic roof and a thick dikelike body along part of the cauldron margin, may be the undrained residue of the magma chamber whose silicic cap was erupted as tuffs and lavas. Small bodies of fine‐grained, porphyritic alkali feldspar granite at the top of the batholith may represent undrained remnants of the silicic cap. Diapirlike intrusions of the deeper, more mafic parts of the batholith into higher more silicic parts may be related to eruption mechanisms. Three younger plutonic phases of the batholith seemingly represent three stages of silicic core magma generation and intrusion during the progressive crystallization and differentiation of the batholith. Major normal faults which offset cauldron fill and are invaded by plutonic rocks suggest the cauldron evolved in a regional extensional stress field.