The 1st International Conference on Oral Mucosal Immunity and the Microbiome (OMIM) took place at the Avra Imperial Hotel, Chania, Crete, Greece, between 26th and 30th September 2018, under the auspices of the Aegean Conferences. This was the first Aegean Conference of its kind in thematic oral research, and a unique blend of immunological and microbiological perspectives, which attracted leading scientists from around the world to discuss the latest advances in the field. The Conference was divided into eight sessions that spanned across 4 days and included the following topics: (a) mucosal barrier immunity; (b) host response and inflammation; (c) microbiome in homeostasis and dysbiosis; (d) fungal and viral pathogenesis; (e) oral microbiome and proteome; (f) microbial virulence and biofilms; (g) microbiome, cancer, and systemic disease; and (h) microbiota and inflammation. There was substantial thematic overlap among all sessions, which promoted constant involvement of the participating scientists. An important hallmark was the active debate between oral microbiologists and oral immunologists, who explored new ideas and potential research collaborations, a crucial aspect for bridging our understanding of oral diseases in the context of the whole body. Key findings are highlighted and thematically presented in the following sections.