Owning to the increase in the world population as well as the consumer’s awareness on the health benefits of consumption of fruits, the demand for both fresh and processed fruits has been increased. The by-product and waste streams generated from fruit processing industries are extremely diverse, owning mainly to different fruits varieties and the wide range of the processes employed towards the production of the end fruit-based products. Due to the increasing production and processing of fruits, disposal of waste and by-product streams is a very significant issue, since these materials are prone to microbial spoilage. Also, inappropriate waste management practices, erase severe environmental issues. Furthermore, costs of drying and storage of fruit processing residues, are economically limiting factors hindering their further exploitation. Therefore, fruit processing by-products such as peels, seeds and unused flesh are often utilized as fertilizers. On the other hand, plant residues contain biomolecules such as vitamins, proteins, minerals, antioxidants and aromatic oil. Recovery of bioactive compounds holds a great potential for their usage in food industry as functional ingredients and nutraceuticals or in pharmaceutical and in cosmetic applications. So, valorization of plant fruit processing by-products to high-value added compounds, constitute a promising alternative not only for addressing fruit residues management issues but also leading to the production of functional food products of high nutritional value, with several potential beneficial health effects. The aim of this paper is to highlight current trends in addressing environmental issues caused by the production of high volumes of specific categories of fruit processing waste streams by investigating their potential usage as natural raw materials for the recovery of valuable bioactive compounds (such as polyphenols, dietary fibers or aromatic oil). The extracted nutrients may be used in industrial food sector for the production of functional foods, nutraceuticals or even as health promoting natural pharmaceutical ingredients or additives for the production of innovative enriched foods.