Background/Aim: Microbial dysbiosis in inflammatory bowel disease (IBD) is poorly understood. Faecal samples collected for the purposes of microbiota analysis are not yet a part of everyday clinical practice. To explore associations between faecal microbiota and disease activity measures in adult IBD patients, for the purpose of possibly integrating microbiota measures in an existing IBD eHealth application for disease-monitoring. Methods: We collected faecal samples from adult IBD patients for one year while they were home-monitoring for disease activity, using faecal calprotectin (FC) and the Simple Clinical Colitis Activity Index (SCCAI). Faecal samples were analysed in two different ways: commercially available test consisting of 54 pre-determined bacterial markers (DNA test) and 16S rRNA gene sequencing (16S-seq). Univariable linear mixed effect models were fitted to predict disease scores using normalised relative abundances as fixed effects. Results: Seventy-eight IBD patients provided a total of 288 faecal samples for microbiota analysis. Two hundred and thirty-four of the samples were from patients with ulcerative colitis (UC). Peptostreptococcus anaerobius was found to correlate significantly with increasing FC, while an additional 24 genera were found to be associated with FC and/or SCCAI (16S-seq). Bacterial markers (DNA test) for Proteobacteria, Shigella spp. and Escherichia spp., were significantly correlated with increasing FC measures, while another 14 markers were found to be associated with FC and/or SCCAI. Conclusions: In patients with UC, results of both methods are associated with disease activity, correlating significantly with Peptostretococcus anaerobius (16S-seq) and with Proteobacteria, Shigella spp. and Escherichia spp. (DNA test).