In the field of stone conservation, the removal of iron stains is one of the most challenging issues due to the stability and low solubility of the ferrous species. In the present paper, three different chitosan-based hydrogels added with acetic, oxalic or citric acids are applied on different lithotypes, i.e., granite, travertine and marble, widely diffused in monumental heritages, and artificially stained by deposition of a rust dispersion. The reducing power of carboxylic acids is combined with the good chelating properties of chitosan to effectively remove rust from stone surfaces. As evidenced by colorimetry on three samples of each lithotype and confirmed by 1H-NMR relaxometry and SEM/EDS analyses, the chitosan-oxalic acid hydrogel shows the best performance and a single application of 24 h is enough to get a good restoration of the stone original features. Lastly, the chitosan-oxalic acid hydrogel performs well when a rusted iron grid is placed directly on the lithic surfaces to simulate a more realistic pollution. Current work in progress is devoted to finding better formulations for marble, which is the most challenging to clean or, with a different approach, to developing protective agents to prevent rust deposition.