Natural bioactive compounds/ biopharmaceuticals with medicinal properties have been beneficial in maintaining a healthy lifestyle since the dawn of humankind. Secondary metabolites are the main bioactive components that are found in large quantities in natural sources, especially plants, animals, and minerals. In the previous several decades, research or exploration into health have proven that consuming bioactive compounds could protect against various diseases, and they are considered better therapeutic agents for treating various ailments. These bioactive compounds can be inherently unstable due to their sensitivity to several in-vitro and in-vivo factors. Hence, proper formulation approaches are crucial to maintaining therapeutic efficacy and bioavailability. Pharmaceutical encapsulation techniques play a vital role in protecting bioactive compounds in relevant aspects. Nanoencapsulation can enhance the stability of bioactive molecules by forming a protective shield, thus improving the pharmacokinetics of drugs at physiologically active sites. This chapter overviews nanoencapsulation techniques and their applications in encapsulating pharmaceutically critical bioactive compounds. It delves into the benefits of nanoencapsulation of bioactive compounds, their properties, and challenges in formulation. It also spotlights the mechanism of nanoencapsulation along with the factors influencing the encapsulation efficiency and release kinetics. Furthermore, it discusses the potential benefits of bioactive compounds in modifying the pharmacokinetic pattern, especially the bio-enhancement of combinational drugs. The chapter also focuses on insights into the current challenges, emerging trends, and future directions in nanoencapsulation research. The chapter will summarize the key findings, reinforcing the potential of nanoencapsulation in advancing the delivery and efficacy of pharmaceutically important biopharmaceuticals.