ABSTRACT Inflammatory bowel disease is associated with complex changes in the intestinal microbiota. While bacterial dysbiosis has been widely studied, the role of fungal communities and their interaction with bacteria remains less explored. This study aims to characterize both bacterial and fungal populations in patients with Crohn's disease and ulcerative colitis, identifying potential microbial biomarkers and inter‐kingdom interactions related to disease activity. We analysed paired intestinal tissue and faecal samples from patients with inflammatory bowel disease. Bacterial, fungal and viral composition were assessed by 16S, ITS DNA and shotgun sequencing, respectively. Bioinformatics analyses were done using Qiime2 and R studio platforms. PERMANOVA and ANOSIM analyses revealed significant compositional differences between faecal and mucosal samples in most groups. Several genera were consistently shared across tissues, while others showed tissue‐ or disease‐specific distributions. Exploratory correlations between bacteria and fungi revealed that Wallemia could play a role in balancing the presence of potentially beneficial and pathogenic bacteria. Importantly, Prevotella was associated with active disease, Fusobacterium with active Crohn's disease, and Roseburia with remission in ulcerative colitis, supporting their potential as biomarkers. All these hypotheses should be further tested in future studies. Our findings reveal distinct microbial signatures in inflammatory bowel disease that could promote the intestinal dysbiosis hypotheses perpetuate chronic intestinal inflammation. The identification of faecal biomarkers may complement approaches for noninvasive monitoring of disease activity. These results underscore the need for further research into bacteria‐fungi interactions and their role in gut inflammation.