The management of industrial fruit by-products is important not only to decrease the volume of food waste accumulated in the landfills but also to develop strategies through reuse with the purpose to valorise and add economic value. The disposal of food waste leads to different global issues in different sectors, such as social, environmental and economical. These by-products represent a rich source of valuable compounds (polyphenols) with high antioxidant activity, which can be extracted through biotechnological methodologies for future industrial applications. In this context, the management of fruit by-products is challenged to move from a linear economy to a circular economy. Therefore, the purpose of this review is to provide a critical view of an integrated valorisation of fruit by-products to overcome a global issue, via the production of antioxidant extracts with high economic value. A case study of pineapple processing industrialization in a circular economy is explored and discussed.