Porous seep-carbonates are exposed at mud volcanoes in the eastern Mediterranean Sea. The 13C-depleted aragonitic carbonates formed as a consequence of the anaerobic oxidation of methane in a shallow sub-surface environment. Besides the macroscopically visible cavernous fabric, extensive carbonate corrosion was revealed by detailed analysis. After erosion of the background sediments, the carbonates became exposed to oxygenated bottom waters that are periodically influenced by the release of methane and upward diffusion of hydrogen sulphide. We suggest that carbonate corrosion resulted from acidity locally produced by aerobic oxidation of methane and hydrogen sulphide in the otherwise, with respect to aragonite, oversaturated bottom waters. Although it remains to be tested whether the mechanisms of carbonate dissolution suggested herein are valid, this study reveals that a better estimate of the significance of corrosion is required to assess the amount of methane-derived carbon that is permanently fixed in seep-carbonates.