Nutraceuticals are natural compounds derived from food substances that provide nutritional and therapeutic benefits. The appropriate processing and optimal storage conditions are essential to maintain the effectiveness of the nutraceuticals for their food value and medicinal advantages. Nutraceuticals’ quality and quantity of active ingredients can vary during processing and storage, and they are affected by various biotic and abiotic factors. This chapter elaborates on the recent progress in understanding nutraceuticals and their processing and storage. First, the current knowledge of nutraceuticals, including their processing and storage, is systematically reviewed. Subsequently, a comprehensive overview of the various environmental factors is provided on the processing and storage of nutraceuticals, for example, abiotic and biotic factors and their discernible impacts on the processing and preservation of nutraceuticals, delving into their underlying mechanisms and repercussions on product stability and functionality. Essentially, understanding the effects of various environmental factors aids in the processing, storage, and preservation of nutraceuticals, thereby enhancing their nutritional value and therapeutic health benefits.