Spinal muscular atrophy (SMA) is an inherited neurodegenerative disease that leads to loss of motor neurons in the anterior horn of the spinal cord with consequent muscle atrophy. SMA results from the functional deletions of the SMN1 gene, resulting in insufficient production of the survival motor neuron (SMN) protein. It is not known why lower motor neurons are particularly sensitive to the loss of SMN function, but it is increasingly apparent that extraneuronal tissues, such as cardiac and skeletal muscle, are also affected by SMN deficiency. We have previously shown that SMN deficiency in a mouse model of spinal muscular atrophy (SMNΔ7) impairs cardiomyocyte contraction and Ca2+ handling. In this study, we performed a comparative total mRNA sequencing analysis of whole hearts isolated at an early (P5) or late (P10) stage of the disease process to investigate the mechanisms contributing to cardiac pathology in SMA. The results demonstrate transcriptional signatures consistent with heart failure, dysregulation of Ca2+ signaling, and hypoxia induced changes occurring as early as P5 and persisting through P10. Similar transcriptomic changes in skeletal muscle tissue indicate that there are likely common, cell autonomous molecular mechanisms resulting in both cardiac and skeletal muscle due to SMN deficiency. The identification of these common themes suggests a link underlying the mechanism of neuronal and non-neuronal deficits in SMA.