The circular economy is an umbrella concept that applies different mechanisms aiming to minimize waste generation, thus decoupling economic growth from natural resources. Each year, an estimated one-third of all food produced is wasted; this is equivalent to 1.3 billion tons of food, which is worth around US$1 trillion or even $2.6 trillion when social and economic costs are included. In the fruit and vegetable sector, 45% of the total produced amount is lost in the production (post-harvest, processing, and distribution) and consumption chains. Therefore, it is necessary to find new technological and environmentally friendly solutions to utilize fruit wastes as new raw materials to develop and scale up the production of high value-added products and ingredients. Considering that the production and consumption of fruits has increased in the last years and following the need to find the sustainable use of different fruit side streams, this work aimed to describe the chemical composition and bioactivity of different fruit seeds consumed worldwide. A comprehensive focus is given on the extraction techniques of water-soluble and lipophilic compounds and functionalities, and the link between chemical composition and observed activity is holistically explained.