The degradation of stone heritage buildings by pioneer plants such as algae is a major challenge in heritage conservation research worldwide. At present, there is a lack of effective algaecides to inhibit the growth of algae on stone structures, prompting an urgent need to explore effective green methods to remove algae colonizing on surfaces of stone heritage buildings. Therefore, we explored the use of aqueous and alcoholic extracts of four plant leaves (Cinnamomum cassia leaf, Syzygium aromaticum leaf, Thymus mongolicus leaf and Pogostemon cablin leaf) to prepare silver nanoparticles. By optimizing the synthetic parameters, we optimized the yield of the nanoparticles and examined their algicidal activities through in-vitro and in-situ experiments. The experimental results showed that the chlorophyll-a concentrations of algae treated with nano-silver synthesized from the alcoholic extract of Cinnamomum cassia leaf decreased approximately threefold, and the algae removal rate reached 71.34%. Meanwhile, nano-silver treatment made the color of the stone chips colonized with algae close to the color of the uncolonized algae, which demonstrated that the nano-silver can effectively remove the algae colonized on the stone chips. This study confirms that nano-silver synthesized from plant leaves offer a viable strategy as a ‘green’ algaecide for stone heritage buildings.