The global prevalence of nutraceuticals is noticeably high with a large market share but minimal regulation compared to traditional drugs. The global market is flooded with nutraceuticals and cosmeceuticals claiming to be of natural origin and sold with a therapeutic claim. In contrast to drugs, which are usually well-defined chemical entities, botanicals are complex ingredients containing multiple chemical components, and often several classes of compounds are present in a single product. Many of these compounds are unstable to heat, light, oxygen, alkaline pH, and elevated humidity. Thus, successful development of nutraceuticals requires knowledge of the fundamental aspects of the physical and chemical properties of the various forms of the ingredients, the use of adequate techniques of manufacturing, selection of the right excipients, and the addition of suitable manufacturing overages based upon critical stability studies. In the recent past, a deluge of interest has developed in the field of nutraceuticals as an alternative source of health. Nanoscale delivery systems have numerous potential applications in the food industry for encapsulating, protecting, and releasing bioactive agents, such as nutraceuticals and vitamins. Nutrients in the form of small solids or droplets improve bioavailability. However, a number of challenges are associated with the enhancement of these dietary supplements from concept to commercialization. The greatest hurdles experienced are the limited shelf life, proper delivery to the targeted sites, and most importantly, ascertaining the overall safety of the nutraceuticals on consumption. The present chapter will highlight the challenges associated with stability, bioavailability, consumer acceptance, and safety evaluation.