Abstract Background The inflammatory bowel disease (iBD) etiology remain elusive and both genetic and environmental factors have been implicated in the establishment of systemic inflammatory reactions that typify IBD. A basic, modifiable environmental factor is the gut microbiota and dysbiosis seems to be a key factor in IBD pathogenesis. Nowadays, it is well known that anti-TNF therapy significantly improves the rates of remission in patients with inflammatory bowel disease (IBD), however, there is a subgroup of patients who do not respond to treatment. The aim of the present study is to profile changes in the mucosal gut microbiome before and after anti-TNF therapy and investigate its possibility to predict patient response at baseline. Methods Mucosal biopsy samples from IBD patients 14 Crohn’s disease patients (CD), 6 ulcerative colitis (UC) patients and healthy controls (HC) were examined for differences in microbiota composition (16S rRNA gene sequencing) at baseline and upon completion of anti-TNF treatment, accordingly, via an in silico pipeline. Results Although no statistically significant differences at phylum level were noted, a relative reduction in Bacteroidetes and an increase in Actinobacteria, Fusobacteria and Chloroflexi were detected in IBD versus HC biopsies, however the microbiomes of UC, CD and HC display qualitative differences at the OTU level. At genus level, statistically significant differential abundance between the HC and IBD groups was observed. The genera Parabacteroides, Barnesiella, Butyricimonas, Ruminococcus_1, Ruminococcaceae_UCG013, Phascolarctobacterium, Ruminoclostridium_6, Paraprevotella as well as members of the Eubacterium_ruminantium group appear reduced in IBD, whereas Dialister abundance is increased. The genus Collinsella exhibits an induction during UC versus both HC and CD. Regarding anti-TNF treatment on the microbiome, Alpha-diversity is reduced after anti-TNF treatment. Beta-diversity indicates differences before and after treatment as well as between responders and non-responders. By using the biomarker discovery tool LEfSe, we identified microbial genera associated mainly with anti-TNF responders. Conclusion In the present study, we showed that the response to anti-TNF therapy is related to specific microbiota profiles in the gut mucosa. Correlation analysis between these parameters of response at baseline showed that the assessment of microbial taxa can further distinguish responders from non-responders.