The purpose of this study was to extract the lipophilic fraction from one of the largest source of waste in the industrial sector, namely, the tomato residue from processing the fruit. In order to make this process more environmentally sustainable, this study used a green extraction protocol employing natural deep eutectic solvents (NADESs) combined with a less energy-consuming technology, the ultrasound-assisted extraction (UAE) method, to simultaneously recover carotenoids and tocopherol from dried powder tomato waste. Two NADESs, one hydrophilic and one hydrophobic, were prepared and compared to support high extraction efficiency and increase the stability of the extracted compounds. The optimal extraction parameters were identified as choline chloride:1,3-butanediol (1:5)-based NADES, a solid-to-liquid ratio of 1:20 (