Bicompartmental Janus particles have many advantages in drug delivery, including co-delivery of two compounds with varying solubilities, differential release kinetics, and two surfaces available for targeting ligands. We present a novel strategy using the double emulsion method for the coencapsulation and staggered release of a hydrophobic and hydrophilic drug from anisotropic PLGA/PCL Janus particles, as well as a UV detection method to measure the release of two different compounds from Janus particles. Curcumin and quercetin were chosen as the model hydrophobic compounds for drug loading studies, while acetaminophen (APAP) and naproxen were chosen as the model hydrophilic–hydrophobic drug pair for encapsulation methods and drug loading. Also, a similar double emulsion method was also applied for PLGA/Preicrol® Janus particles containing Doxorubicin and Curcumin. Hydrophobic drugs were encapsulated by the single O/W emulsion technique. Hydrophilic compounds required special modifications due to their poor oil solubility and tendency to escape to the outer aqueous phase during the emulsification and solvent evaporation steps. In total, three different strategies for incorporating hydrophilic drugs were employed: (1) O/W emulsion with partially water miscible solvent, (2) O/W emulsion with co-solvent (i.e. acetone, methanol, ethanol), or (3) W/O/W double emulsion. The encapsulation efficiencies and drug loading percentages were measured using UV/Vis spectroscopy and compared for the different synthesis methods. It was found that the double emulsion method resulted in the highest encapsulation efficiency and drug loading of the hydrophilic drug.