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Aligned with the EU Sustainable Development Goals 2030 (EU SDG2030), extensive research is dedicated to enhancing the sustainable use of biomass waste for the extraction of pharmaceutical and nutritional compounds, such as (poly-)phenolic compounds (PC). This study proposes an innovative one-step hydrothermal extraction (HTE) at a high temperature (120 °C), utilizing environmentally friendly acidic natural deep eutectic solvents (NADESs) to replace conventional harmful pre-treatment chemicals and organic solvents. Brewer's spent grain (BSG) and novel malt dust (MD) biomass sources, both obtained from beer production, were characterized and studied for their potential as PC sources. HTE, paired with mild acidic malic acid/choline chloride (MA) NADES, was compared against conventional (heated and stirred maceration) and modern (microwave-assisted extraction; MAE) state-of-the-art extraction methods. The quantification of key PC in BSG and MD using liquid chromatography (HPLC) indicated that the combination of elevated temperatures and acidic NADES could provide significant improvements in PC extraction yields ranging from 251% (MD-MAC-MA: 29.3 µg/g; MD-HTE-MA: 103 µg/g) to 381% (BSG-MAC-MA: 78 µg/g; BSG-HTE-MA: 375 µg/g). The superior extraction capacity of MA NADES over non-acidic NADES (glycerol/choline chloride) and a traditional organic solvent mixture (acetone/H 2 O) could be attributed to in situ acid-catalysed pre-treatment facilitating the release of bound PC from lignin-hemicellulose structures. Qualitative 13 C-NMR and pyro-GC-MS analysis was used to verify lignin-hemicellulose breakdown during extraction and the impact of high-temperature MA NADES extraction on the lignin-hemicellulose structure. This in situ acid NADES-catalysed high-temperature pre-treatment during PC extraction offers a potential green pre-treatment for use in cascade valorisation strategies (e.g., lignin valorisation), enabling more intensive usage of available biomass waste stream resources.