Glycogen storage disease type II (GSDII), caused by a genetic defect in acid alpha-glucosidase (AGLU), leads to a decline in muscle contractility caused by both muscle wasting and a decrease in muscle quality, i.e., force generated per unit muscle mass. A previous study has shown that loss of muscle mass can only explain one-third of the decrease in contractile performance. Here we report on changes in the intramyocellular structural organization in a mouse knockout model (AGLU(-/-) mice) as a possible cause for the decline in muscle quality. Swollen, glycogen-filled lysosomes and centrally localized cores with cellular debris partially contribute to the decline in muscle quality. Altered localization and deposition of cytoskeletal proteins desmin and titin may reflect adaptive mechanisms at the age of 13 months, but a decline in quality at 20 months of age. The early deposition of lipofuscin in AGLU-deficient myocytes (13 months) is most likely a reflection of enhanced oxidative stress, which may also affect muscle quality. These collective findings, on the one hand, may explain the decrease in tissue quality and, on the other, may represent markers for efficacy of therapeutic interventions to restore muscle function in patients suffering from GSDII.