Coffee and cocoa agribusinesses generate large volumes of byproducts, including coffee husk, coffee pulp, parchment skin, silver skin, and cocoa bean shell. Despite the rich composition of these materials, studies on biomolecule extraction with green solvents are still scarce, and further research is needed. Extraction methods using alternative solvents to obtain biomolecules must be developed to enhance the byproducts' value and align with biorefinery concepts. This article reviews the compositions of coffee and cocoa byproducts, their potential applications, and biomolecule extraction methods, focusing on alternative solvents. The extraction methods currently studied include microwave-assisted, ultrasound-assisted, pulsed electric field-assisted, supercritical fluid, and pressurized liquid extraction. At the same time, the alternative solvents encompass the biobased ones, supercritical fluids, supramolecular, ionic liquids, and eutectic solvents. Considering the biomolecule caffeine, using alternative solvents such as pressurized ethanol, supercritical carbon dioxide, ionic liquids, and supramolecular solvents resulted in extraction yields of 2.5 to 3.3, 4.7, 5.1, and 1.1 times higher than conventional solvents. Similarly, natural deep eutectic solvents led to a chlorogenic acid extraction yield 84 times higher than water. The results of this research provide a basis for the development of environmentally friendly and efficient biomolecule extraction methods, improving the utilization of agricultural waste.