Background: Exercise is an important component of a healthy lifestyle, the development of which is a relapse prevention strategy for those with alcohol use disorder. However, it is a challenge to create exercise interventions with a persistent behavioural change. The aim of this qualitative study was to investigate perceived barriers to participation in an exercise intervention among alcohol use disorder patients, who dropped out of the intervention program. Furthermore, this study aims to propose possibilities for a better practice of future intervention studies based on the participants’ experiences and suggestions. Methods: Qualitative interviews with 17 patients who dropped out from an exercise intervention in an outpatient treatment centre about their experiences and reasons for dropping out. Social cognitive theory informed the development of the interview guides and systematic text condensation was used for analysis. Results: Analysis revealed three central themes: 1) Structural barriers described as the type of exercise and the timing of the intervention, 2) Social barriers described as need for accountability and unsupportive relations, and 3) Emotional barriers described as fear, guilt and shame, and negative affect of the intervention on long term. Conclusions: Future exercise interventions should include socio-psychological support during the first weeks, begin shortly after treatment initiation instead of concurrently, and focus on garnering social support for participants in both the intervention context and among their existing network in order to best reduce barriers to participation. Trial registration: This study was retrospectively registered at Current Controlled Trials ISRCTN74889852 on 11 July 2013.