Background: Crohn’s disease (CD) is a chronic inflammatory bowel disease frequently associated with malabsorption and secondary protein-energy malnutrition (PEM). Methods: Biochemical and clinical data of 63 (34 females, 29 males) patients with PEM due to CD sent to our outpatient unit for nutritional evaluation were retrospectively analyzed. Patients were divided into two groups, according to disease activity. Thirty-eight patients (group A) had the active disease, and 25 patients (group B) suffered from malabsorption resulting from past intestinal resections due to CD. After a physical and hemato-biochemical evaluation at the first visit, all patients received disease-specific personalized dietetic indications. When indicated, oral nutritional supplements, oral/parenteral vitamins, micronutrients, and electrolytes, up to parenteral nutrition, were prescribed. Results: After 1, 3, and 6 months of nutritional therapy, body weight, body mass index (BMI), and serum butyryl-cholinesterase significantly improved in both groups. In 8 out of 13 (61.5%) patients with a cutaneous stoma, intestinal continuity was restored. Conclusions: This study confirms the effectiveness of nutritional rehabilitation and provides information on the time required for nutritional treatment in patients with CD, both during the acute phase and after malabsorption due to intestinal resection.