A pre-restoration diagnosis revealed a high amount of pyrite in the wood of the Lyon Saint-Georges 4 shipwreck (end of the second century). The occurrence of this phase is supposed to result from the microbiologically influenced corrosion of the iron fasteners. So, all the nails and metallic elements were removed from the remains before treatment and the wreck was consolidated by polyethylene glycol impregnation coupled to a specific desalination process. Treated and non-treated samples extracted from the wreck were studied in order to identify the iron/sulfur-containing compounds present in the wood before and after treatment and figure out its effect. Sample analyses relied on an original approach combining magnetic characterization methods and more common elemental and structural analysis methods. The results showed that the treatment was effective in removing soluble salts. However, a large amount of unstable iron sulfides remained inside the wood.