Sea cucumbers have high economic value, and in most forms of trade, their body wall is typically the only part that is harvested and sold. The organs of the sea cucumber, collectively known as the viscera, are frequently discarded, contributing to land and water pollution. However, discarded sea cucumber viscera contain various nutrients that can be used in many applications. Therefore, this review highlights the biological and economic aspects of sea cucumbers, followed by a critical discussion of the nutritional value of their internal organs and possible applications, including as functional feed additives in the aquaculture industry, sources of natural testosterone for application in sex reversal and production of monosex population, of neuroprotective agents against central nervous system disorders and of cosmetic ingredients, especially for skin whitening and anti-ageing products. The review further highlights the valorisation potential of viscera to maximize their economic potential, thus providing an enormous prospect for reusing sea cucumber waste, thereby reducing the negative impact of the sea cucumber fishery sector on the environment.