Abstract Objectives Children with short bowel syndrome (SBS) are at increased risk of micronutrient deficiencies. We aimed to study weaning off parenteral nutrition (PN) as a risk factor for vitamin and trace element deficiencies and growth deficit. Methods Children born between 2010 and 2019, treated for SBS in Helsinki University Hospital, were followed for their nutrition, growth, and vitamin and trace element biochemical status. Information on these as well as patient characteristics and intestinal anatomy were collected from electronic patient records. Results A total of 59 patients with SBS were identified. The weaning period was found to be a risk factor for micronutrient deficiencies and growth. Most frequent deficiencies were detected for vitamin K as suggested by prothrombin time (PT) (91% of patients), vitamin D (70%), and vitamin A (67%). Other deficiencies were less common with 44% for vitamin B12, 25% for selenium, 19% for copper, 24% for zinc, and 11% for vitamin E. For all the studied micronutrients, 3 months before to 1 month postweaning had the highest rate of micronutrient deficiencies, except for vitamin B12, for which the highest proportion of deficiencies presented at 1–6 months postweaning. Conclusions The weaning period from PN is a risk for micronutrient deficiencies. Regular monitoring and sufficient supplementation are essential for preventing malnutrition.