Carbon mobilization in hydrothermal sediments and advective transport of dissolved organic matter (DOM) to the ocean affect deep-sea ecosystems. However, the link between hydrothermal processes and DOM reactivity in organic-rich subsurface sediments, and the impact of DOM release on the marine carbon cycle remain poorly understood. The Guaymas Basin (Gulf of California), with its organic-rich sediments, hydrothermal vent sites, and magmatic sill intrusions is an ideal candidate for studying the hydrothermal influences on DOM biogeochemistry. We analyzed sediment and porewater samples from IODP Expedition 385 from down to ∼330 m below seafloor and used hot-water Soxhlet extractions as a first-order approximation for simulating hydrothermal DOM mobilization. We assessed the molecular composition of solid-phase extractable (SPE) DOM via ultrahigh-resolution mass spectrometry (FT-ICR-MS) and quantified dissolved organic sulfur, nitrogen, and phosphorus (DOSSPE, DONSPE, DOPSPE). We identified several biogeochemical processes transforming DOM: active microbial transformations in the upper sediments were related to enhanced DOM oxygenation, and elevated DONSPE and DOPSPE concentrations. Highly aromatic, probably recalcitrant DOM, accumulated under anoxic conditions in intermediate depths. Here, DOSSPE concentrations were highest, probably due to abiotic sulfide incorporation into DOM. Hydrothermal alteration near magmatic sills reduced DOM molecular diversity and caused a significant shift in the chemical composition of deep subsurface sediments influenced by high temperatures. Our data indicated that hydrothermal sediments release DOM, including DOSSPE, DONSPE and DOPSPE, to the ocean. Hence, hydrothermal discharge may not only sustain local benthic ecosystems by providing bioavailable DOM but also likely influences the deep-sea carbon pool by introducing recalcitrant DOM.