Spaceflights significantly impacts astronaut health, causing muscle atrophy, bone loss, cardiovascular deconditioning and immune system dysregulation, especially during long missions. To explore molecular changes, we generated a single-cell RNA sequencing dataset, of 216 samples from 28 mouse organs and tissues under spaceflight and control conditions. Since spaceflight effects closely resemble aspects of aging, we included two age groups (3 and 8 months) to assess age-related influences. Our data revealed that spaceflight drives age-independent systemic changes, primarily affecting tissue remodeling and alterations in cytoskeleton, membrane and extracellular matrix (ECM), particularly in endothelial cells. In contrast, aging has a weaker impact, mainly altering immune regulation in an age-dependent manner. These findings suggest that cytoskeletal and ECM changes may contribute to immune Dysregulation.