Rocks from the 23 Ma Lake City caldera show diverse chemical affinities attesting to a complex magmatic system beneath the caldera. Field and geochemical data from ignimbrites and intrusions constrain magma storage and magma interactions during the formation of the caldera. Two geochemically distinct magma batches erupted during caldera formation: batch A, consisting of rhyolites and trachytes, and batch B, consisting of dacites and trachyandesites. The ignimbrites of the Lower, Middle, and Upper Sunshine Peak Tuff represent the bulk of erupted batch A magma, with an increasing proportion of trachyte to rhyolite as the eruption progressed. Overall, the observed trends of major and trace elements are consistent with the sequential eruption of a magmatic system with a rhyolitic upper portion and trachytic lower portion. The Middle Sunshine Peak Tuff contains two distinct types of pumice clast, while the Upper Sunshine Peak Tuff contains four distinct pumice clast types, with one type chemically related to batch B magma. The link between the rhyolite and trachyte of batch A is supported by major- and trace-element geochemical modeling of an initially trachytic magma that fractionated and was subjected to crystal/melt segregation following 50%–60% crystallization. Compositional gaps and chemical heterogeneity in the bulk ignimbrite composition show that the proportions of these different magma types varied significantly during eruption. We propose that the fractionating batch A and B magmas formed distinct magma pods, some containing residual magma mush, that were tapped during different phases of caldera formation. After collapse, dacite lavas of batch B were erupted concurrent with resurgent uplift from shallow intrusion of both residual mingled batch A and batch B magma. In summary, our observations suggest (1) a complex magma chamber geometry from two fractionating magma batches, and (2) magma replenishment and accelerated periods of magma reorganization in the shallow magma plumbing system during a single caldera cycle at Lake City.