Abstract Objectives The present randomized controlled study aimed to evaluate the effects of two interventions on emotional dysregulation as a primary outcome and on depression, anxiety, stress, well‐being, self‐compassion and emotional competencies as secondary outcomes. Finally, the mediating role of emotional dysregulation as a core process in the effect of interventions on anxiety‐depressive and stress symptoms was evaluated. Methods One hundred and seventy‐nine individuals aged 18–68 years ( M = 39, SD = 12.4; 83.9% females) with emotion regulation difficulties were randomly assigned to one of the three 12‐weeks online programs: Compassion Focused Program (CFP), an Emotional Competencies Program (ECP) or a Waitlist control condition (WL). Participants completed pre‐, post‐ and 3 months follow‐up measures of each outcome. Mixed effect linear models compared groups on primary and secondary outcomes. Results Results showed that (1) perceived credibility and expectancy and satisfaction did not differ between the two interventions, (2) both interventions reduced emotion regulation difficulty, depression, anxiety and stress symptoms, and enhanced well‐being, self‐compassion, and emotional competencies; (3) ECP was more effective to enhance well‐being than CFP; (4) CFP was more effective to enhance emotional competencies than ECP, and (5) emotion regulation difficulty mediated the effect of the interventions on depression, anxiety, and stress symptoms. Conclusions Findings offer preliminary support for the usefulness of online CFP and ECP to reduce emotion dysregulation, symptoms of depression, anxiety, and stress and to increase well‐being, self‐compassion and emotional competencies. These results are discussed regarding clinical practice and the transdiagnostic role of emotional dysregulation.