Raw coffee beans are seen as valuable sources of bioactive compounds, such as alkaloids and chlorogenic acids. In this study, an efficient and eco-friendly method for the simultaneous extraction of caffeine, trigonelline, and chlorogenic acids from raw beans of two coffee species was developed, using green solvents and an unconventional method of extraction (assisted by ultrafast rotary disintegrator/homogenizer (UT-AE)). The experimental extraction conditions were optimized according to a completely randomized design (CRD), considering the following variables: solvent type (four deep eutectic solvents (DESs), water, and aqueous choline chloride solution (50 wt.%); temperature (25, 45, and 65 °C); and extraction technique (solid-liquid extraction with agitated heating and assisted by ultrafast rotary disintegrator/homogenizer). The extract obtained with choline chloride solution (50 wt.%) exhibited high total phenolic compounds and the highest antioxidant capacity. An analysis using high-performance liquid chromatography with a diode array detector (HPLC-DAD) indicated the presence of chlorogenic acids, caffeine, and trigonelline in all the extracts, in different amounts. The results obtained by the analysis of phenolic compounds and HPLC indicated that the aqueous solution of choline chloride (50% wt.%) was the most suitable solvent for the extraction of chlorogenic acids, while the water-based extracts showed high values of caffeine and trigonelline. DESs, in turn, seems to promote a protective effect on the antioxidant activity of biomolecules.