SummaryThe research focused on the recovery of bioactive compounds from beetroot waste (fresh stalks) using an innovative and microwave‐mediated (mw) procedure that could allow the simultaneous eutectic solvent preparation and matrix extraction (in situ mw NADES extraction), as a simplification of more conventional NADES (natural deep eutectic solvents) extractions. The main goal was to propose a fast and simple “one‐pot” extractive approach to obtain and screen non‐toxic, bioactive ready‐to‐use ingredients, potentially useful in food, cosmetic and pharmaceutical fields, meanwhile converting beetroot residues, from worn‐out plant matrices to recycled sources with significant added values. With this purpose, several eutectic mixtures of natural food‐grade hydrogen bond donors (choline chloride or betaine) and hydrogen bond acceptors (fructose, urea, citric acid, and glycerol) were selected and investigated (in opportune ratios) under microwave activation, considering time, temperature, and solvent‐to‐matrix ratio as the influencing variables and the total phenols content recovery as the response. By the in situ NADES microwave method developed, the best results were obtained within 5 min at 70 °C with recoveries of around 0.5 mg of polyphenols for gram of fresh stalks, assessed by the Folin–Ciocalteu test. The suitability of the NADES‐based extractives, as radical scavenging agents, was evaluated using the DPPH assay, which highlighted their good antioxidant activity; moreover, monitoring the betacyanin content by means of UV–vis spectrophotometric analyses, it was evident that NADES provide a relevant stability to the new complexes (up to 3 months) compared to water (24 h). The new in situ process proposed could be also useful for preliminary screenings of different organic matrices, simplifying workup, streamlining the procedures, and reducing costs.