Gut microbiota dynamically participate in diverse physiological activities with direct impact on the host's health. A range of factors associated with the highly complex intestinal flora ecosystem poses challenges in regulating the homeostasis of microbiota. The consumption of live probiotic bacteria, in principle, can address these challenges and confer health benefits. In this context, one of the major problems is ensuring the survival of probiotic cells when faced with physical and chemical assaults during their intake and subsequent gastrointestinal passage to the gut. Advances in the field have focused on improving conventional encapsulation techniques in the microscale to achieve high cell viability, gastric and temperature resistance, and longer shelf lives. However, these microencapsulation approaches are known to have limitations with possible difficulties in clinical translation. In this Perspective, we present a brief overview of the current progress of different probiotic encapsulation methods and highlight the contemporary and emerging single-cell encapsulation strategies using nanocoatings for individual probiotic cells. Finally, we discuss the relative advantages of various nanoencapsulation approaches and the future trend toward developing coated probiotics with advanced features and health benefits.