Tomato pomace (TP) has previously been identified as a coproduct that is rich in bioactive molecules, with potential beneficial effects for health. For tomato pomace that is composed of the skin, seeds and fibers, the challenge is to recover the molecules of interest trapped in the biopolymers. The use of deep eutectic solvents to extract metabolites from vegetable materials could present some advantages. Four natural deep eutectic solvents (NaDESs) were synthesized and characterized by infrared spectroscopy, thermogravimetry (TG) and differential scanning calorimetry (DSC). The TP was treated by maceration at moderate temperatures with the NaDESs. We identified 39 extracted molecules by HPLC–DAD, which revealed an abundance of hydroxy/methoxy flavones, flavanols, flavonols, phenolic acids, carotenoids and tannins, as well as a certain selectivity in the extracted molecules. Four cosmetic formulations that included the NaDESs were prepared. The NaDESs showed film-forming properties, which were harnessed for the final formulations, thanks to their biocompatibilities. Finally, the coupling of the extraction and formulation is a way to preserve the quality of the extracts and prepare ecodesigned formulations.