Heteroprotein complex coacervation (HPCC) is a phenomenon of liquid–liquid phase separation in which oppositely charged proteins interact to form a coacervate phase (rich in proteins) that will be in equilibrium with a diluted phase, known as equilibrium solution. Among the different applications of the HPCC, the encapsulation of bioactive compounds has gained special attention due to the potential of these coacervates to protect and improve the bioaccessibility of the target compounds. Nonetheless, several parameters, such as pH, ionic strength, and concentration of the involved molecules, play an important role in the mechanism of complex coacervation. In this context, this chapter will discuss the main methods applied to study the potential of heteroprotein complex coacervates as a vehicle for encapsulating bioactive compounds. The different methods were divided into three segments: (i) characterization of the molecular interaction between the target molecules, (ii) micro and mesoscopic aspects of the formation of complex coacervates, and (iii) coacervation yield and encapsulation efficiency. The principle of the different methods, the experimental protocol, and some insights for data processing will be detailed.