An innovative bio method was investigated to extract harmful iron and sulfur species from waterlogged wood samples. The method was compared with a chemical treatment. Both approaches were applied on lacustrine and marine samples, from different wood genera, to evaluate the versatility of the proposed bio method. Non-invasive and non-destructive methods were carried out to investigate both bio-based and chemical treatments. The result was that some wood genera were more affected by the bio approach, with a clear distinction between lacustrine beech and pine against oak and lime wood species. The chemical approach showed potential harm for the wooden structure, with acidic pH values and an increase of maximum water content, both implying degradation of the wood structure. In terms of extraction, no iron or sulfur products were detected by Raman spectroscopy on biologically treated samples, in agreement with extraction rates calculated. It was also suggested that iron bonded to wood was extracted with the chemical approach, and calcium content affected by both approaches.