This dataset includes the data obtained from a study carried out from 2019 to 2021 at the Sant Joan de Deu Hospital (Esplugues de Llobregat, Barcelona). The study analyzes the metagenomics of a set of paediatric patients affected by inflammatory bowel disease (IBD). A pilot study of oral and faecal microbiota was proposed with 36 paediatric patients divided in three cohorts (12 with Crohn's Disease (CD), 12 with Ulcerative Colitis (UC) and 12 healthy controls [HC]) with 6 months of follow-up. Finally, 30 participants were included: 13 with CD, 11 with UC and 8 HC (6 dropped out during follow-up). Despite the small size of the study population, a differential pattern of microbial biodiversity was observed between IBD patients and the control group. Twenty-one bacterial species were selected in function of their discriminant accuracy, forming three sets of potential markers of IBD. Although IBD diagnosis requires comprehensive medical evaluation, the findings of this study show that faecal metagenomics or a reduced set of bacterial markers could be useful as a non-invasive tool for an easier and earlier diagnosis.