The nature of sub-volcanic alteration is usually only observable after erosion and exhumation at old inactive volcanoes, via geochemical changes in hydrothermal fluids sampled at the surface, via relatively low-resolution geophysical methods or can be inferred from erupted products. These methods are spatially or temporally removed from the real subsurface and thus provide only indirect information. In contrast, the ICDP deep drilling of the Mt Unzen volcano subsurface affords a snapshot into the in situ interaction between the dacitic dykes that fed dome-forming eruptions and the sub-volcanic hydrothermal system, where the most recent lava dome eruption occurred between 1990 and 1995. Here, we analyse drill core samples from hole USDP-4, constraining their degree and type of alteration. We identify and characterize two clay alteration stages: (1) an unusual argillic alteration infill of fractured or partially dissolved plagioclase and hornblende phenocryst domains with kaolinite and Reichweite 1 illite (70)-smectite and (2) propylitic alteration of amphibole and biotite phenocrysts with the fracture-hosted precipitation of chlorite, sulfide and carbonate minerals. These observations imply that the early clay-forming fluid was acidic and probably had a magmatic component, which is indicated for the fluids related to the second chlorite-carbonate stage by our stable carbon and oxygen isotope data. The porosity in the dyke samples is dominantly fracture-hosted, and fracture-filling mineralization is common, suggesting that the dykes were fractured during magma transport, emplacement and cooling, and that subsequent permeable circulation of hydrothermal fluids led to pore clogging and potential partial sealing of the pore network on a timescale of ~ 9 years from cessation of the last eruption. These observations, in concert with evidence that intermediate, crystal-bearing magmas are susceptible to fracturing during ascent and emplacement, lead us to suggest that arc volcanoes enclosed in highly fractured country rock are susceptible to rapid hydrothermal circulation and alteration, with implications for the development of fluid flow, mineralization, stress regime and volcanic edifice structural stability. We explore these possibilities in the context of alteration at other similar volcanoes.