Micronutrient deficiencies are common in patients with inflammatory bowel disease (IBD), but whether they relate to disease outcomes remains unknown. This study assessed the micronutrient status of adults with IBD on treatment with biologic therapies and explored predictive relationships with disease outcomes. Seventeen micronutrients were measured in the blood of 216 adults with IBD on biologic therapy. Of these, 127 patients (58%) had Crohn's disease (CD), and the majority (70%) received treatment with infliximab. Patients were followed for 12 months and onset of adverse clinical outcomes (eg, requirement for treatment with corticosteroids, hospitalization, or surgical intervention) was recorded, and related to micronutrient status. Among all patients, the most common deficiencies were for vitamin C (n = 35 of 212 [16.5%]), ferritin (n = 27 of 189 [14.3%]), folate (n = 24 of 171 [14.0%]), and zinc (n = 27 of 210 [12.9%]). During follow-up, 22 (10%) of the 216 patients developed 1 or more adverse clinical outcomes. Patients with CD and zinc deficiency were significantly more likely to require surgery (P = .002) or treatment with corticosteroids (P < .001). In contrast, patients with ulcerative colitis and selenium deficiency were significantly more likely to have a clinical flare of disease (P = .001), whereas those with CD were not. This relationship with selenium remained significant after adjustment for confounders. A substantial proportion of adults with IBD present deficiencies for certain micronutrients, with selenium and zinc deficiency predicting adverse disease outcomes. For other micronutrients, deficiencies were less common and should not warrant routine screening. Intervention studies should explore the effect of micronutrient supplementation in modifying disease outcomes in IBD.