Current data and models for Mount St. Helens volcano (Washington, United States) suggest relatively rapid transport from magma genesis to eruption, with no evidence for protracted storage or recycling of magmas. However, we show here that complex zircon age populations extending back hundreds of thousands of years from eruption age indicate that magmas regularly stall in the crust, cool and crystallize beneath the volcano, and are then rejuvenated and incorporated by hotter, young magmas on their way to the surface. Estimated dissolution times suggest that entrained zircon generally resided in rejuvenating magmas for no more than about a century. Zircon elemental compositions reflect the increasing influence of mafic input into the system through time, recording growth from hotter, less evolved magmas tens of thousands of years prior to the appearance of mafic magmas at the surface, or changes in whole-rock geochemistry and petrology, and providing a new, time-correlated record of this evolution independent of the eruption history. Zircon data thus reveal the history of the hidden, long-lived intrusive portion of the Mount St. Helens system, where melt and crystals are stored for as long as hundreds of thousands of years and interact with fresh influxes of magmas that traverse the intrusive reservoir before erupting.