Spinal muscular atrophy (SMA) is a devastating recessive neurological disorder thought to be affecting primarily the motor neurons. As such, paralysis, motor weakness and death ensue. While SMA is most commonly seen in infants and children, it can span all ages. Its genetic etiology revolves around the homozygous deletion or mutation of the SMN1 gene, whose product (SMN protein) has critical and ubiquitous roles in mRNA splicing, amongst various other functions in mRNA metabolism. As such, SMN depletion in other non-neuronal cells type is likely to have physiological repercussions, and perhaps modulate the SMA phenotype. Herein, we identify the molecular pathways of atrophy in skeletal and cardiac muscle of two mouse models of SMA and their therapeutic modulation via the histone deacetylase inhibitor trichostatin A. We also identify dramatic changes in immune organs in mouse models of SMA, which could impact susceptibility to infections. Furthermore, we establish the presence of important defects in fatty acid homeostasis in the liver and plasma seen in both mouse models and SMA patients. Finally, we provide the first mild mouse model of SMA that reliably reproduces canonical features of SMA, permitting aging studies. This model presents with a prominent myopathic phenotype prior to motor neuron death, without extra-neuronal involvement during the course of its lifespan. Overall, our work shows multiple potentially clinically relevant defects in extra-neuronal organs, provides ways to abrogate them and provides a framework to study them over the course of aging.