Cocoa (Theobroma cacao L.) and its derivatives are appreciated for their aroma, color, and healthy properties, and are commodities of high economic value worldwide. Wide ranges of conventional methods have been used for years to guarantee cocoa quality. Recently, however, demand for global cocoa and the requirements of sensory, functional, and safety cocoa attributes have changed. On the one hand, society and health authorities are increasingly demanding new more accurate quality control tests, including not only the analysis of physicochemical and sensory parameters, but also determinations of functional compounds and contaminants (some of which come in trace quantities). On the other hand, increased production forces industries to seek quality control techniques based on fast, nondestructive online methods. Finally, an increase in global cocoa demand and a consequent rise in prices can lead to future cases of fraud. For this reason, new analytes, technologies, and ways to analyze data are being researched, developed, and implemented into research or quality laboratories to control cocoa quality and authenticity. The main advances made in destructive techniques focus on developing new and more sensitive methods such as chromatographic analysis to detect metabolites and contaminants in trace quantities. These methods are used to assess cocoa quality; study new functional properties; control cocoa authenticity; or detect frequent emerging frauds. Regarding nondestructive methods, spectroscopy is the most explored technique, which is conducted within the near infrared range, and also within the medium infrared range to a lesser extent. It is applied mainly in the postharvest stage of cocoa beans to analyze different biochemical parameters or to assess the authenticity of cocoa and its derivatives.