Patients with COPD suffer from lower-limb muscle dysfunction characterized by lower muscle oxidative capacity and muscle mass. Exercise-based training is expected to attenuate lower-limb intramuscular characteristics, but a detailed systematic approach to review the available evidence has not been performed yet. PUBMED and PEDro databases were searched. Twenty-five studies that implemented an exercise-based training program (aerobic and/or resistance training, high intensity interval training, electrical or magnetic stimulation) and reported muscle biopsy data of patients with COPD were critically appraised. The coverage of results includes changes in muscle structure, muscle protein turnover regulation, mitochondrial enzyme activity, oxidative and nitrosative stress, and inflammation after exercise-based training interventions. Study design and training modalities varied among studies, which partly explains the observed heterogeneous response in muscle characteristics. Gaps in the current knowledge are identified and recommendations for future research are made to enhance our knowledge on exercise training effects in patients with COPD.