Nano-magnetite is a potential archive for biosignatures and paleoenvironmental proxies in hydrothermal systems. However, sulfidic diagenesis at hydrothermal conditions potentially drives the rapid transformation of magnetite to Fe sulfide minerals. The identity and characteristics of transformation products from these reactions are crucial for interpreting biosignature records and paleoenvironmental proxies associated with Fe minerals in sulfide deposits. To constrain the preservation and transformation of magnetite in hydrothermal sulfide habitats, we incubated synthetic nano-magnetite in anoxic artificial seawater at a sulfide:Fe ratio of 4:1 as well as at different pH (7, 10) and temperatures (20-80°C), and in presence or absence of added S0. Experimental products were analyzed by means of sequential Fe extraction, μ-X-ray diffraction (μ-XRD), Raman spectroscopy, and scanning electron microscopy (SEM). After 46 days, nano-magnetite was only detected at 20°C (pH ∼10). Fe(III)-containing mackinawite and greigite formed at pH ∼10 and ≥20°C. At pH ∼7 and 80°C, magnetite was transformed to pyrite within only 19 days, with faster rates in the presence of polysulfides, which formed from the sulfide-mediated reduction of Fe(III) and in the presence of S0. Our results demonstrate a potential taphonomic bias against nano-magnetite in sulfidic hydrothermal habitats and suggest that pyrite-associated paleoenvironmental proxies and biosignature records of Fe- and S-cycling microorganisms in hydrothermal deposits are affected by diagenetic fluid-mineral interactions.