The Protected Denomination of Origin (PDO) and Protected Geographic Indication (PGI) labels were established to legally protect traditional cheeses, particularly those derived from small ruminants’ milk, through the definition of strict production standards. Nevertheless, the impact of certification has often fallen short of initial expectations in terms of sector valorisation and rural development. Increasing the economic sustainability of traditional small ruminants’ raw milk cheeses requires scaling without compromising their distinctive identity. In this context, increasingly stringent regulations on the hygiene and disinfection practices associated with milk refrigeration have significantly affected the characteristic properties of these cheeses, which are largely shaped by traditional manufacturing practices and the indigenous milk microbiota. This review synthesises distinctive attributes of Spanish and Portuguese PDO/PGI cheeses and emphasises the roles of cardoon (Cynara spp.) extracts and small ruminants’ raw milk microbiota in influencing the proteolysis, lipolysis, texture and flavour of such cheeses. Variability in cardoon ecotypes, enzyme activity, and microbial composition strongly affects cheese texture, aroma, and safety. Key challenges include inconsistent coagulant quality, the hygienic constraints associated with raw milk, regulatory limitations, and restricted market access. This review outlines strategies to address these challenges, including the standardisation and selection of elite cardoon ecotypes, improved milk hygiene practices, the development of tailored starter and non-starter cultures, and risk-based regulatory approaches. These measures are crucial to preserve authenticity while ensuring safety and economic resilience, thereby reinforcing the role of Iberian PDO/PGI cheeses in sustaining small ruminant dairy systems and rural economies.