Activated carbon (AC) is widely used in ecological studies for neutralizing allelopathic compounds. However, it has been suggested that AC has direct effects on plants because it alters substrate parameters such as nutrient availability and pH. These side-effects of AC addition may interfere with allelopathic effects. In this study we analyzed three widely used commercial AC brands and analyzed their effect on pH, their ability to retain glucosinolates, and their effect on the germination of six plant species. AC brands differed significantly in their effect on pH values when added to different substrates. Glucosinolates were completely adsorbed by all brands, indicating that AC is suitable as adsorbent for this compound class. Finally, AC addition to substrates had differential effects on seed germination of Arabidopsis thaliana, Plantago lanceolata, Solidago canadensis, and Lotus corniculatus, whereas no effect was found on the germination of Lactuca sativa and Brassica oleracea. We suggest that scientists using AC should always include an experimental control to test for direct effects of AC addition on both substrate parameters and plant performance.