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The growing demand for more sustainable, alternative processes leading to production of plant-derived preparations imposes the use of plants waste generated mainly by agri-food and pharmaceutical industries. These mostly unexploited but large quantities of plants waste also increase the interest in developing alternative approaches for sustainable production of therapeutic molecules. In order to reduce the amount of plant waste by further processing, different novel extraction techniques can be applied. Fruits and their industrial by-products are rich sources of different classes of compounds with therapeutic properties. The processed fruits waste can be reused and lead to novel pharmaceuticals, food supplements or functional foods. This review intends to briefly summarize recent aspects regarding the production of different active compounds from fruit by-products, and their therapeutic properties. The potential use of fruits by-products in different industries will be also discussed.