ACTA1 encodes skeletal muscle-specific alpha-actin, which polymerizes to form the thin filament of the sarcomere, and mutations in ACTA1 are responsible for roughly 30% of nemaline myopathy (NM) cases. Acta1 animal models have been generated including the Acta1 H40Y (H40Y) and the Acta1 D286G (D286G) murine models. Previous studies of weakness in NM have focused on skeletal muscle structure and contractility, however, genetic causes do not fully explain the significant phenotypic heterogeneity observed in NM patients or mouse models. Due to this, proteomic analysis of muscles from moderately affected H40Y and the minimally affected D286G Acta1 mouse models was performed against their WT counterparts to identify disease-relevant secondary biological processes. This analysis revealed abnormalities in mitochondrial function and stress-related pathways in both models. Importantly, mitochondria-associated proteins were affected differently between the two mouse models, suggesting that mitochondrial function is differentially impaired by different Acta1 mutations. Histological evaluation showed generally appropriate morphology in D286G animals and severe abnormalities of protein aggregation and mitochondrial mislocalization in the H40Y mice. Mitochondrial respirometry revealed no differences between D286G and WT mice, but a significant impairment was detected in H40Y mice specifically at 6-weeks of age. Changes in the amount of ATP, ADP, or phosphate present in tissue extracts were found in both H40Y and D286G muscles relative to WT. This was not accompanied by differences in electron transport chain enzyme function. Overall, the severity of biochemical and morphological changes reflects differences in disease severity between the H40Y and D286 mouse models. Our results imply that NM has an energetic deficiency that may correlate with disease severity, opening new directions for studies related to NM classification and treatment targets.