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AAS treatment is a very efficient method to increase the methane potential of manure fibers. The chemical composition and supramolecular structures of swine manure fibers before and after AAS treatment was investigated in this study. Composition analyses, atomic force microscopy (AFM), scanning electron microscopy (SEM), and chemical surface composition by Attenuated Total Reflectance–Fourier Transform Infrared (ATR–FTIR) showed that no delignification of the lignocellulose took place during AAS-treatment. Instead, the fibers were cleansed from debris, thus leaving the cellulose more exposed and accessible during subsequent anaerobic digestion. This finding has confirmed earlier experimental results, showing that delignification was not necessarily the limiting factor during conversion of manure fibers into methane while cellulose accessibility during digestion seemed more crucial.