Babassu (Orbignya phalerata) is a valuable oleaginous fruit in Brazil’s economy. After processing to extract oil, large quantities of residual mesocarp are generated. Typically, this by-product finds reuse as an additive in animal feed or is sold as flour for human consumption. However, there is a pressing need for innovative approaches to valorize this residue and leverage new technologies to create value-added compounds. Most existing processes for lignocellulosic biomass suffer from low selectivity during pre-treatment, often neglecting essential fractions like lignin, which holds significant biotechnological potential. In this context, deep eutectic solvents (DES) have emerged as a promising alternative pre-treatment method, thanks to their remarkable properties, including the ability to solubilize lignin, recyclability, and catalytic capacity. This study investigates the dissolution of residual babassu mesocarp in various deep eutectic solvents at different temperatures (70–130 °C) and biomass:solvent ratios (0.05−0.1). Two initial candidates, choline chloride:acetic acid (CC:AA) and proline:acetic acid (PRO:AA), were chosen. Notably, CC:AA achieved an impressive dissolution yield of up to 97.6% by mass of the residual mesocarp, while PRO:AA reached up to 50.8% by mass, with the thermal effect proving highly significant. Interestingly, the biomass:solvent ratio showed minimal influence on dissolution yield. The analysis of liquid fractions revealed that, for CC:AA treatment, lignin content measured 2.3 mg/mL (70 °C), 9.8 mg/mL (100 °C), and 10.5 mg/mL (130 °C). In contrast, PRO:AA treatment resulted in lignin content of 3.1 mg/mL (70 °C), 2.3 mg/mL (100 °C), and 2.8 mg/mL (130 °C). Furthermore, PRO:AA treatment yielded a total carbohydrate concentration of 2.2 mg/mL (70 °C), 1.9 mg/mL (100 °C), and 3.9 mg/mL (130 °C). For CC:AA treatment, the respective values were 2.6 mg/mL (70 °C), 17.2 mg/mL (100 °C), and 29.6 mg/mL (130 °C). UV/VIS analyses confirmed the dissolution of lignin and hinted at the extraction of tannins and anthocyanins (in CC:AA), underscoring their catalytic potential. This study marks the initial step in dissolving babassu mesocarp in DES and presents a promising avenue for biomass valorization in the future.