Nutraceuticals and nanonutraceuticals are the functional ingredients that supplement nutrients in daily diet intake for health-related benefits. Nutraceuticals contain bioactive ingredients such as vitamins, minerals, amino acids, pre- and pro-biotics, spices, and herbs. Moreover, these are also categorized as hydrophilic (vitamins and mineral salts), lipophilic (omega-3 oil), amphiphilic (peptides), or those components which are insoluble in water as well as oil (probiotics). Notably, numerous bioactive substances are unstable when isolated from their natural products and could suffer from ineffective targeting, poor solubility, and low permeability. Thus, these ingredients are formulated to protect them from degradation and undesirable interactions, to increase their shelf life, and beneficial efficacy. For the same, delivery systems are designed for effective nutraceutical consumption. A thorough and pinned knowledge of active ingredients, their properties, interactions in the body and with the environment, functions, storage, and form of consumption are required for the successful delivery of nutraceuticals. The beneficial effects of nutraceuticals can also be amplified with appropriately designed delivery systems. These delivery systems not only improve the stability but enhance the function and performance of nutraceuticals and nanonutraceuticals in the body. Unfortunately, several challenges are associated with the designing and development of appropriate delivery systems for nutraceuticals. In this chapter, the designing and development of delivery systems and their associated challenges have been discussed.