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The gut microbiome is a diverse microbial community composed of bacteria, viruses, and fungi that plays a major role in human health and disease. Dysregulation of these gut organisms in a genetically susceptible host is fundamental to the pathogenesis of inflammatory bowel disease (IBD). While bacterial dysbiosis has been a predominant focus of research for many years, there is growing recognition that fungal interactions with the host immune system are an important driver of gut inflammation. <i>Candida albicans</i> is likely the most studied fungus in the context of IBD, being a near universal gut commensal in humans and also a major barrier-invasive pathogen. There is emerging evidence that intra-strain variation in <i>C. albicans</i> virulence factors exerts a critical influence on IBD pathophysiology. In this review, we describe the immunological impacts of variations in <i>C. lbicans</i> colonisation, morphology, genetics, and proteomics in IBD, as well as the clinical and therapeutic implications.