In view of the increasing evidence that commonly prescribed, non-antibiotic drugs interact with the gut microbiome, we re-examined the microbiota variance in inflammatory bowel disease (IBD) to determine the degree to which medication and supplement intake might account for compositional differences between disease subtypes and geographic location. We assessed the confounding effects of various treatments on the faecal microbiota composition (16S rRNA gene sequencing) in persons with Crohn's disease (CD; n = 188) or ulcerative colitis (UC; n = 161) from either Cork (Ireland) or Manitoba (Canada) sampled at three time points. The medication profiles between persons with UC and CD and from different countries varied in number and type of drugs taken. Among Canadian participants with CD, surgical resection and overall medication and supplement usage is significantly more common than for their Irish counterparts. Treatments explained more microbiota variance (3.5%) than all other factors combined (2.4%) and 40 of the 78 tested medications and supplements showed significant associations with at least one taxon in the gut microbiota. However, while treatments accounted for a relatively small proportion of the geographic contribution to microbiome variance between Irish and Canadian participants, additive effects from multiple medications contributed significantly to microbiome differences between UC and CD.