Abstract Background More than 10% of the global population has a BMI above 35. Bariatric surgery is an efficient way to treat this condition. Unfortunately, there is a risk of nutritional deficiencies. The number of studies after a longer time span is scarce. The aim of this study was to determine the occurrence of anaemia five and ten years after bariatric surgery and how it was related to substitution therapy. Patients and methods Registry data from individuals having primary bariatric surgery in the Scandinavian Obesity Surgery Registry (SOReg) from 2007 to 2022 and with a follow-up at five or ten years was retrieved. Demographic data including weight, as well as method of surgery, Hb levels, supplementation, PPI use and stomal ulcerations were recorded. Results In total, 39,992 individuals (mean age 41 years, range 18–74, 77% women) could be included. The majority, 78%, had undergone laparoscopic Roux-en-Y gastric bypass. After five years, 2838/13,944 women (20.3%) and 456/4049 men (11.2%) had anaemia. After ten years, 644/3400 women (18.9%) and 178/947 men (18.8%) had anaemia. The use of oral iron increased from 40 to 45%, and the need for parenteral iron intake increased from 5 to 11%. Conclusions Anaemia is a significant but manageable condition five and ten years after bariatric surgery. Despite the prescription of oral iron supplements to 45% ten years after surgery, the Hb levels could still not be fully restored. Consequently, the importance of follow-up visits and continuous supplementation is emphasised.