BiomeHealth aims to strengthen European and Portuguese R&I on agro-food systems that face climate change and new/recurrent pathogens, with the support of Wageningen Univ. & Research (WUR, NL) and Bologna Univ. (UNIBO, IT). Global trade and climate change favor the establishment of new pathogens in Europe. Portugal needs to boost R&I and education/training to empower a new generation of researchers in this field. BiomeHealth has two R&I objectives, and four capacitation objectives aligned with the Twinning call. WUR (precision pathogens detection), and UNIBO [VOC-biosensors, Biological Control Agents, and SynComs] will develop R&I and capacitation of the widening partner, Requimte/UP that leads the national research in agrifood. This capacitation networking will use groundbreaking concepts of plant microbiome, precision detection, and engineering of synthetic communities (SynComs) of BCAs (supported by artificial intelligence, AI). BiomeHealth structure has six interdependent WPs: WP1 is for Coordination and Management; WP2 deals with R&I on precision detection and control of phytobiomes also challenged by climate change (as a case study we will use Pear/Apple trees under an RCP8.5 climatic scenario, and challenged with Erwinia amylovora, and Stemphylium vesicarium). New detection tools/matrices (e.g., aerobiomes), dynamics host-microbiome-pathogen, and SynComs, will be unveiled/tested for the RCP8.5 condition. WP3 (precision detection) and WP4 (Control using SynComs) are dedicated to the capacitation of Requimte/UP, with dedicated short-term visits, training/advanced courses, summer schools, etc. WP5 will build a sustainable structure through a R&I roadmap of Requimte/UP for 2030, and the creation of a Centre of Plant Pathogen Detection and Control. Finally, WP6 deals with dissemination/communication. This 36-month twinning will boost the precision detection/control of diseases in Portugal, increasing its networking competitiveness and international recognition.