Waste produced during cultivation of edible plants can be a valuable source of bioactive molecules. Herein, we present the valorization of tomato leaves to obtain biologically active extracts. Deep eutectic solvents (DESs), composed of natural ingredients, were applied as extracting solvents. The extracts were rich in bioactive chemicals such as phenolics and flavonoids, with rutin as the main component (∼6 mg/g of biomass). The obtained extracts showed high antioxidative potential. Moreover, it was possible to recycle DES for subsequent extractions. Evaluation of the antimicrobial activity of the extracts against selected bacteria (Escherichia coli and Staphylococcus epidermidis) and yeast (Candida albicans) revealed that it showed strong antifungal activity, while the pure solvent did not exhibit such properties. The study revealed that by adhering to the principles of the circular economy and extracting waste tomato leaves using natural DESs, valuable antioxidants and antimicrobial agents can be obtained with high yields.