For thousands of years, the interaction between the human nutrition, genome and microbiome led populations to be biologically adapted to certain diets. Although this entangled coevolution is a key aspect of sustainable and healthy alimentation, the majority of our scientific knowledge is restricted to European populations, increasing inequality between Western and developing countries. In Oceania, Papua New Guineans (PNG) are the descendants of a 50,000 years long interaction with a unique environment from which they extracted specific food resources. They managed their environment until the independent invention of agricultural practices around 8,000 years ago. Despite this intricate history with local resources, modern PNG populations often suffer from malnutrition especially in urban places where industrialized food is mostly consumed. The NUTRIOCEO project is built on the ambition to characterize in depth the genome-microbiome-diet interaction in PNG, using a multidisciplinary approach combining expertise from nutritional anthropology, genomics, and microbiology. Based on a long-term international collaboration, we will analyse human genomic variants, oral and gut microbiome diversity and dietary data for 300 participants from PNG in rural and urban locations. The main objectives are (1) to characterize the genetic adaptations caused by historical changes in diets in PNG; (2) to determine the oral and gut microbial diversity in PNG and its link to diet; (3) to identify associations between genetic variants under selection and microbial species associated with diet; (4) to evaluate the impact of urban diet on the interaction genome-microbiome-diet. The NUTRIOCEO project will unveil coevolutionary mechanisms of important matter regarding human health in our era marked by climate changes and the problematic of the availability of alimentary resources.