New technologies are in development regarding the preservation of waterlogged archaeological wood items contaminated with Fe/S species. To this purpose, a bio-based treatment to extract these harmful species before further damages occur is presented. Thiobacillus denitrificans and desferoxamine were employed based on their specific properties to solubilize iron sulfides and uptake iron. The biological treatment was compared with oxidizing and complexing agents (sodium persulfate and ethylene diamine tetraacetate) traditionally used in conservation-restoration. Mock-ups of fresh balsa as well as fresh and archeological oak and pinewood were prepared to simulate degraded waterlogged wood by immersion in corrosive Fe/S solutions. The efficiency of both biological and chemical extraction methods was evaluated through ATR-FTIR and Raman spectroscopies and validated by statistical approach. Results showed that treatments did not affect the wood composition, meaning that no wood degradation was induced. However, the chemical method tended to bleach the samples and after treatment, reduced sulfur species were still identified by Raman analyses. Finally, statistical approaches allowed validating ATR-FTIR results