The human gut microbiome has been implicated in the pathogenesis of inflammatory bowel disease (IBD), but most research in this area has focussed heavily on prokaryotes (bacteria and archaea) to the exclusion of other members of the gut microbiome such as eukaryotes (fungi and protozoa). The aim of our study was to characterise the often-neglected eukaryotic gut microbiome in patients with IBD. We scanned for fungi and protozoa in shotgun metagenomes from stool samples originating from 355 IBD patients and 471 unaffected individuals. The IBD patients had a higher abundance and diversity of fungi, particularly Saccharomyces, and a lower abundance of protozoa. Interestingly, we found that Blastocystis species were more abundant in the healthy individuals than IBD patients. Blastocystis species have been historically viewed as a gastroenteritis-causing group of protozoan pathogens, but more recent work, including our present study, suggests that they are innocuous microbes that indicate a healthy and diverse gut microbiome. By including eukaryotes, our study provides a more comprehensive understanding of the IBD-biome, which is critically important as gut microbiome-altering therapies such as faecal transplantation continue to rise in popularity for treating IBD.