Experimental studies have provided convincing evidence that food bioactive compounds (FBCs) have a positive biological impact on human health, exerting protective effects against non-communicable diseases (NCD) including cancer and cardiovascular (CVDs), metabolic, and neurodegenerative disorders (NDDs). These benefits have been associated with the presence of secondary metabolites, namely polyphenols, glucosinolates, carotenoids, terpenoids, alkaloids, saponins, vitamins, and fibres, among others, derived from their antioxidant, antiatherogenic, anti-inflammatory, antimicrobial, antithrombotic, cardioprotective, and vasodilator properties. Polyphenols as one of the most abundant classes of bioactive compounds present in plant-based foods emerge as a promising approach for the development of efficacious preventive agents against NCDs with reduced side effects. The aim of this review is to present comprehensive and deep insights into the potential of polyphenols, from their chemical structure classification and biosynthesis to preventive effects on NCDs, namely cancer, CVDs, and NDDS. The challenge of polyphenols bioavailability and bioaccessibility will be explored in addition to useful industrial and environmental applications. Advanced and emerging extraction techniques will be highlighted and the high-resolution analytical techniques used for FBCs characterization, identification, and quantification will be considered.