Objective This 15 years longitudinal study aimed to examine whether difficulties in cognitive processing of emotions persisted after long‐term recovery from anorexia nervosa (AN), and its link to anxiety and depression. Method Twenty‐four females, who were tested longitudinally during their acute and recovered AN phases, and 24 healthy control (HC) women, were screened for anxiety, depression, alexithymia, emotion regulation difficulties (ER; only assessed in recovery phase), and completed an experimental task to analyse emotional experience. Results In spite of significant improvement in alexithymia, anxiety, and depression with AN recovery, some emotion functioning difficulties did not normalize. The occurrence of comorbid anxiety and depression explained the reduced ability to identify, understand, and accept emotions in long‐term recovery (relative to controls), but not the increased global difficulty in using ER strategies, which revealed a more stable nature of deficit. With recovery, negative emotions linked to situations addressing food and body weight are felt more intensely. Conclusions Managing emotions, especially the negative ones, remains a challenge for individuals recovered from AN. Under this circumstance, maladaptive eating behaviour can serve as an affect regulatory function, increasing the risk of relapse. Emotional education is an important avenue in protecting long‐term AN relapse.