Safe and efficient processing of plant-based bioproducts increasingly relies on process-intensified and automated operations. In this work, for the first time a deep eutectic solvent (DES)-based flow platform was engineered for fully automated extraction and quantification of key bioactive classes, polysaccharides and polyphenolic antioxidants in functional plant materials. Arctium lappa L. root was used as a representative food-grade matrix. The system integrates ultrasound-assisted extraction in a thermostated manifold, in-syringe colour development, and on-line UV-Vis detection, followed by HPLC-UV profiling of polyphenols from the same DES extract. Among seven tested DES formulations, choline chloride-ethylene glycol was selected as the optimal medium. Process intensification was achieved by tuning the DES hydration level and by statistical optimisation of temperature and extraction time using response surface methodology, yielding 10.5 mg g−1 of polysaccharides at 65 °C and 40 min. Molecular dynamics simulations provided quantitative insight into polysaccharide-DES interactions and demonstrated that moderate hydration preserves the eutectic structure while enhancing molecular mobility, rationalizing the experimentally observed maximum at 30 wt% water. The automated procedure was validated for β-glucan and inulin, showing excellent linearity (R2 = 0.9972–0.9976), low limits of detection (0.0008–0.012 mg g−1), high recoveries (98–99 %) and good precision (RSD ≤ 4.7 %). Compared with methanol extraction, the DES-based process delivered higher recoveries of polyphenolic antioxidants. The validated method was successfully applied to the analysis of burdock root and other cereal matrices (oat grass, pearl flour), showing excellent agreement with a standard enzymatic reference method. Greenness assessment using the AGREE tool confirmed reduced solvent consumption, limited waste generation and improved operator safety. The proposed platform extends the boundaries of food and bioproducts processing by combining green solvent design, process intensification and automation for routine characterisation of functional plant bioproducts.