The enrichment of the stable isotopes 13C and 15N across trophic levels is a commonly used tool in studies on organic matter flow and food webs. An accepted standard for pre-analysis sample preparation, however, is still missing. Thus, potential methodological bias in single studies may hamper comparability and scalability of data from different sources. Sample CaCO3 content introduces a positive bias in ?13C measurements and a negative bias in ?15N measurements. The acidification of samples to remove inorganic carbonate significantly reduces both ?13C and ?15N. As a standard procedure we recommend (i) to acidify samples with as little hydrochloric acid (HCl) as possible using the drop-by-drop technique and (ii) to restrain from rinsing after HCl application.