INTRODUCTION: Anorexia nervosa (AN) is a complex psychiatric disorder, which can lead to specific somatic complications. Undernutrition is a major diagnostic criteria of AN and it can be associated with several micronutrients deficiencies. OBJECTIVES: This study aimed to determinate the prevalence of micronutrients deficiencies and to compare the differences between the two subtypes of AN (restricting type (AN-R) and binge-eating/purging type (AN-BP)). METHODS: We report a large retrospective, monocentric study of patients that were hospitalized in a highly specialized AN inpatient unit between January 2011 and August 2017 for severe malnutrition treatment in the context of anorexia nervosa. RESULTS: Three hundred and seventy-four patients were included, at inclusion, with a mean Body Mass Index (BMI) of 12.5 ± 1.7 kg/m². Zinc had the highest deficiency prevalence 64.3%, followed by vitamin D (54.2%), copper (37.1%), selenium (20.5%), vitamin B1 (15%), vitamin B12 (4.7%), and vitamin B9 (8.9%). Patients with AN-BP type had longer disease duration history, were older, and had a lower left ventricular ejection fraction (LVEF) (p < 0.001, p = 0.029, p = 0.009) when compared with AN-R type patients who, instead, had significantly higher Alanine Aminotransferase (ALT) and Brain Natriuretic Peptide (BNP) levels (p < 0.001, p < 0.021). In the AN-BP subgroup, as compared to AN-R, lower selenium (p < 0.001) and vitamin B12 plasma concentration (p < 0.036) was observed, whereas lower copper plasma concentration was observed in patients with AN-R type (p < 0.022). No significant differences were observed for zinc, vitamin B9, vitamin D, and vitamin B1 concentrations between the two types of AN patients. CONCLUSION: Severely malnourished AN patients have many micronutrient deficiencies. Micronutrients status must be monitored and supplemented to prevent deficiency related complications and to improve nutritional status. Prospective studies are needed to explore the symptoms and consequences of each deficiency, which can aggravate the prognosis during recovery.