Abstract Inflammatory bowel disease (IBD) is a class of chronic inflammatory gut disorders whose aetiogenesis is still unknown. Despite the high number of omics studies, the RNA sequencing (RNA-Seq) data produced for a better IBD pathogenesis understanding cannot be compared because of the experimental variability and different data analysis approaches. To overcome this hurdle, we here introduce the open-source IBD Transcriptome and Metatranscriptome Meta-Analysis (TaMMA) framework, a comprehensive survey of publicly available IBD RNA-Seq datasets. IBD TaMMA will expedite the profiling of the IBD-associated transcriptome and metatranscriptome, holding out the strong promise of being of high impact for the IBD community.