Slowly progressive proximal muscle weakness in an otherwise healthy male posed particular challenges for the treating physicians, considering the wide range of possible differentials. Here we present a case of a 52-year-old male with paraparesis, elevated creatine kinase-levels, antibodies against the Mi-2 antigen and subtle skin lesions, leading to subsequent treatment for dermatomyositis. Beyond that, exome sequencing revealed biallelic variants in the gene encoding acid alpha-glucosidase with concordant reduced enzymatic activity in fibroblasts, indicating late onset Pompe disease. Subsequently performed magnetic resonance imaging revealed a pattern of involvement typical for LOPD, but histological workup from the vastus lateralis muscle was more indicative of an immune-mediated myopathy. After treatment for dermatomyositis and Pompe disease the patient showed an improvement in skin changes and a halt in muscular weakness. In conclusion, both entities could be seen in the patient. However, early and prolonged subclinical hyper-CK-emia hinted at Pompe disease as the primary entity.