Cynara cardunculus health benefits have aroused much interest, leading to the discovery of valuable bioactive compounds with a crucial role in plant defence. Guaianolides and hydroxycinnamic acids, mainly represented by cynaropicrin and chlorogenic acid, constitute the major secondary metabolites in leaves (9.5% and 10.4% dry weight, respectively). These compounds evidence biological activity, namely antioxidant, antitumoral, hepatoprotective, antimicrobial and anti-hyperlipidemic effects. Therefore, numerous efforts have been undertaken in this species to unveil the biosynthetic pathways of such compounds, by means of genomic and biochemical approaches, which could support advances, via breeding programs, in C. cardunculus chemical composition and, consequently, in the improvement of its extracts biological activity. Addressing this challenge, relevant genes in cynaropicrin biosynthesis, as well as in chlorogenic acid biosynthesis have been widely studied. The present review highlights the current knowledge on the biosynthesis and distribution of guaianolides and hydroxycinnamic acids, especially of cynaropicrin and chlorogenic acid in C. cardunculus, as well as their association with plant defence mechanisms and human health-promoting effects, prospecting the valorisation of this Mediterranean species as a potential source of bioactive compounds for food, nutraceutical and pharmaceutical purposes.