Aquaculture has grown steadily in recent decades in the Mediterranean, particularly Sparus aurata (gilthead seabream) and Dicentrarchus labrax (European seabass), which represent 25% of European aquaculture production value. Sustainable aquaculture is a vital component of the Farm-to-Fork strategy, promoting both environmental stewardship and economic prosperity. However, most fish production is conducted in open cages, which inevitably leads to exposure to pathogens, representing a significant and growing risk for the industry. Therefore, the early detection of diseases is of the utmost importance. While recent advancements in early detection tools have seen a shift from traditional methods to molecular and probe-based diagnostics – enhancing the specificity, sensitivity, and speed of pathogen identification – they are still insufficient to avoid major production losses. Their application is fairly limited due to a lack of robust databases to support them. Moreover, emerging pathogens or alterations in pathogens antimicrobial resistance profiles pose a considerable threat to aquaculture, impacting both the health of aquatic species and economic sustainability. Further, the development of efficient immune-boosting solutions to control diseases are paramount for fish welfare. Continuous research and development of new diagnostic technologies and vaccine-like solutions are essential to achieve the EU goal of accelerating the transition to a sustainable food system. AquaMed’s objective is to fill in the knowledge gaps on pathogens impacting seabream and seabass farming by creating swift, precise, and dependable diagnostic tools based on MALDI-TOF and ddPCR, with the ultimate goal of developing immunisation-like solutions through the encapsulation of immunogenic peptides. This is a promising and innovative approach for enhancing disease management in aquaculture and ensuring the industries’ sustainability while improving animal welfare.