Inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis, have a complex and multifactorial pathogenesis that remains not fully elucidated. Recent research suggests that intestinal fungal dysbiosis may contribute to the development and persistence of IBD. In this study, we explored, for the first time, the effects of the glucocorticoid-induced leucine zipper (GILZ) protein, known to have protective effects on the gut mucosa in preclinical IBD models, in combination with a yeast extract, which supports the growth of beneficial microorganisms, in a mouse model of ulcerative colitis. The combined treatment produced significant protection against severe disease outcomes in the mice, including the restoration of intestinal barrier integrity and the reduction of pro-inflammatory cytokines. Specifically, GILZ primarily acted on the gut permeability, while the yeast extract mainly reduced pro-inflammatory cytokines. Notably, both treatments were effective in restoring the intestinal burden of clinically importantCandidaand formerCandidaspecies. Analysis of the intestinal fungal communities revealed that both treatments were able to reduce colitis-associated fungal dysbiosis, promoting a fungal composition similar to that of healthy mice. This effect was mainly the result of a decreased abundance of theMeyerozimagenus, which was dominant in the colitic mice. Thus, combined treatment regimens with the GILZ protein and yeast extract could represent a new strategy for the treatment of inflammatory bowel diseases, by targeting multiple mechanisms at the basis of IBD, including the fungal dysbiosis.IMPORTANCEInflammatory bowel diseases (IBD), including Crohn’s disease and ulcerative colitis, are characterized by chronic inflammation and have a complex, multifactorial pathogenesis that is not yet fully understood. Currently, no established therapeutic strategy can consistently manage IBD effectively. Recent research indicates that intestinal fungal dysbiosis could potentially contribute to the development and persistence of chronic IBD, highlighting the importance of investigating alternative therapeutic strategies able to attenuate fungal dysbiosis in the context of intestinal inflammation. In this study, we demonstrate that a combination of a recombinant protein (GILZp) and a compound with prebiotic properties could represent a new therapeutic strategy for the treatment of IBD, as it not only decreases inflammation and restores the integrity of the epithelial barrier, but reduces fungal dysbiosis associated with DSS-induced colitis.