Nano-magnetite is a potential archive for biosignatures of iron-cycling microorganisms in hydrothermal systems, which are widely considered to be among the most ancient microbial habitats on Earth. Sulfidic diagenesis driven by hydrothermal fluids and microbial sulfur cycling potentially causes the rapid transformation of magnetite to iron sulfide minerals. Thus, identifying nano-magnetite and its transformation products in hydrothermal sulfide deposits is crucial for reconstructing iron- and sulfur-cycling microbial life in deep time. However, the identity and characteristics of iron sulfide minerals resulting from nano-magnetite sulfidation at hydrothermal conditions have previously not been constrained. Here we present experimental data on sulfidation reactions of synthetic and biogenic nano-magnetite at physical and chemical conditions relevant to microbial habitats in hydrothermal systems on early Earth (<121°C, anoxic, sulfidic). We characterize the resulting precipitates with analytical imaging techniques, mineralogical methods, and geochemical approaches (e.g., SEM-EDS, µXRD, Raman spectroscopy, sequential Fe extraction). Our results demonstrate a potential taphonomic bias against nano-magnetite in sulfidic hydrothermal habitats and suggest that biosignature records of iron- and sulfur-cycling microorganisms in ancient hydrothermal sulfides are affected by diagenetic fluid-mineral interactions.