In October 2025, the Trends in Host-Microbe Symbioses Symposium at the University of Padova (Italy) brought together a global community of researchers, with the aim of taking stock of the current trajectory of marine host-microbiome research. Integrating perspectives from ecology, evolution, biogeochemistry, and biotechnology, the symposium documented a clear transition from descriptive surveys of microbial diversity toward a mechanistic understanding of host–microbe interactions. Across an unusually broad taxonomic spectrum—corals, sponges, fishes, molluscs, algae and seagrasses, cnidarians, acoels, arthropods and mammals—microbiomes were consistently framed as integral components of host biology, shaping nutrient cycling, development, immunity, and ecosystem function. Despite phylogenetic diversity across host groups, convergent functional processes (notably N and C cycling, stress buffering, immune priming, and metabolic complementation) emerged as a unifying framework, even though their taxonomic underpinnings remained system-specific. Advances in multi-omics, spatially resolved imaging (MALDI-MSI, NanoSIMS, FISH/CARD-FISH) and experimental microbiome manipulation are increasingly linking microbial identity to activity and function, enabling early predictive frameworks across scales. Collectively, the symposium laid the groundwork for microbiome-based interventions to enhance host resilience and support ecosystem conservation in a rapidly changing ocean.