Both under-and over-nutrition are prevalent in patients with Crohn’s Disease (CD). The aim of the present study was to evaluate dietary intake and compare it with relevant recommendations during active disease and remission, also taking into consideration the adequacy of energy reporting. Dietary quality was assessed through adherence to the Mediterranean diet and to the European dietary guidelines for cardiovascular disease prevention (CVD-score). Malnutrition was diagnosed with the GLIM criteria. There were 237 patients evaluated (54.9% males, 41.3 ± 14.1 years and 37.6% with active disease). In the total sample, high prevalence of overweight/obesity (61.6%) and low prevalence of malnutrition (11.4%) were observed, whereas 25.5% reported low protein intake in the sub-sample of adequate energy reporters. The mean MedDietScore was 28.0 ± 5.5 and the mean CVD-score was 5.25 ± 1.36, both reflecting moderate dietary quality. Patients with active disease reported higher prevalence of low protein intake, lower carbohydrate, fibers, fruits, vegetables, legumes, and sweets consumption and a lower MedDietScore compared to patients in remission. Consumption of fibers, fruits, vegetables, and legumes while in remission did not result in reaching the recommended intakes, and dietary quality was low as reflected by the MedDietScore. In conclusion, both protein undernutrition and energy overconsumption were prevalent in the current sample and overall patients adhered to a moderate quality diet irrespective of disease stage.