Non-extractable polyphenols (NEPs), or bound polyphenols, are a significant fraction of polyphenols that are retained in the extraction residues after conventional aqueous organic solvent extraction. They include both high molecular weight polymeric polyphenols and low molecular weight phenolics attached to macromolecules. Current knowledge proved that these bioactive compounds possess high antioxidant, antidiabetic, and other biological activities. Plant-based food by-products, such as peels, pomace, and seeds, possess high amount of NEPs. The recovery of these valuable compounds is considered an effective way to recycle food by-products and mitigate pollution, bad manufacturing practice, and economic loss caused by the residues management. The current challenge to valorise NEPs from plant-based by-products is to increase the extraction efficiency with proper techniques, choose appropriate characterising methods, and explore potential functions to use in some products. Based on this scenario, the present review aims to summarise the extraction procedure and technologies applied to recover NEPs from plant-based by-products. Furthermore, it also describes the main techniques used for the characterisation of NEPs and outlines their potential food, pharmaceutical, nutraceutical, and cosmetic applications.