Emotional dysregulation is a key transdiagnostic dimension of several clinical conditions, including eating disorders (EDs) and gender dysphoria (GD). Not only is there frequent comorbidity between EDs and GD, but GD individuals also commonly experience ED symptoms and body-image disturbances. However, more research is needed to understand how specific body-related experiences may differently interact with difficulties in emotion regulation and dysfunctional eating behaviors in EDs and GD. Thus, the present study aimed at exploring potential associations between emotional dysregulation and ED symptomatology in individuals diagnosed with anorexia nervosa (AN), bulimia nervosa (BN), or gender dysphoria (GD), also considering the mediating role of specific dimensions of body uneasiness. A national sample of N = 96 help-seekers assigned female at birth (n = 32 with AN, n = 32 with BN, n = 32 with GD) was recruited from two specialized care centers. Participants completed the Eating Disorder Inventory-3 (EDI-3) and the Body Uneasiness Test (BUT), while the Shedler-Westen Assessment Procedure–200 (SWAP-200) was used to evaluate emotional dysregulation. Findings showed that several body uneasiness dimensions mediated the relationship between emotional dysregulation and ED symptoms, in both AN-BN and GD participants. In GD individuals, body avoidance emerged as a significant mediator of the relationship between emotional dysregulation and ED symptoms, whereas in both AN-BN patients and GD individuals, depersonalization toward the body emerged as a significant mediator. The results suggest that the interplay between emotional dysregulation, body uneasiness, and ED symptoms may be crucial for the development of comprehensive and tailored prevention strategies.