Crohn’s disease (CD) is associated with increased cardiovascular risk and the retinal microcirculation is a reflection of the systemic microcirculation. Is the retinal microcirculation altered in relation to the severity of Crohn’s disease? This cross-sectional case-controlled study was conducted in a university hospital center from November 2020 to February 2021. We prospectively included patients with moderate (biologic therapy) or severe (biologic therapy + peri-anal disease and/or digestive resection) CD and age- and sex-matched controls. Individuals with diabetes, renal disease, cardiovascular disease, ophthalmological history or poor quality images were excluded. All participants underwent OCT angiography (OCT-A) imaging (Optovue, Fremont, CA). Analysis of covariance was used. 74 CD patients (33 moderate, 41 severe) and 74 controls (66 (44.6%) men; mean (SD) age 44 (14) years) were included. Compared with the controls, the severe CD patients showed a significantly reduced mean foveal avascular zone area (p = 0.001), superficial macular capillary plexus vessel density (p = 0.009) and parafoveal thickness (p < 0.001), with no difference in mean superficial capillary flow index (p = 0.06) or deep macular capillary plexus vessel density (p = 0.67). The mean foveal avascular zone was significantly lower in the severe than the moderate CD patients (p = 0.010). OCT-A can detect alterations in retinal microcirculation in patients with severe versus moderate CD and versus age- and sex-matched controls.