The brewing properties of coffee products are defined by the chemical composition in the bean, including sugars and polyols. Some factors, such as coffee species and roasting, may affect the level of these compounds in the bean. A new analytical microwave-assisted extraction (MAE) method has been developed to extract sugars and polyols from the coffee bean. The studied extraction conditions for the MAE were temperature (30–80 °C), solvent composition (0–50% ethanol in water), and solvent-to-sample ratio (10:1–30:1 mL solvent per g sample). A Box-Behnken design was applied to study the effect of extraction variables, and subsequently, the influential variables were optimized by response surface methodology (RSM). In addition to the main effect of the solvent-to-sample ratio, all quadratic effects significantly influenced (p < 0.05) the recovery of sugars and polyols from the coffee beans. RSM suggested the optimized MAE conditions: temperature 52 °C, ethanol concentration in water 18.5%, and solvent-to-sample ratio 17:1. Under the optimum condition, a kinetics study confirmed that 15 min showed high precision and accuracy of the developed method. Ultimately, a real sample application of the developed MAE revealed that the new method successfully described the composition of sugars and polyols in regular and peaberry coffee beans. Additionally, the method also effectively characterized the green and roasted Arabica and Robusta coffee beans.