Production of coffee beans is an important lifeline for the economy of several countries in Latin America, Africa, and Asia. The brew from this well sought for cash crop is readily consumed due to its good sensory qualities owing to the presence of many micronutrients. Some of these chemical compounds possess biological activities, including antiproliferative, antioxidant, and antimicrobial effects. Four representative groups of these micronutrients, namely, caffeine, chlorogenic acid, diterpenes, and trigonelline, play key roles in these bioactive effects of coffee. In order to guarantee the quality of coffee products and to protect consumer interest and safeguard their well-being, it is extremely important to employ sensitive and accurate analytical methods in the characterization and quantitative determination of these bioactive constituents. This review aims to present recent applications in this regard.