Updated project metadata. Sporadic and familial amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease that results in loss of motor neurons and, in some patients, associates with frontotemporal dementia (FTD). Apart from the accumulation of proteinaceous deposits, an emerging literature indicates that aberrant mitochondrial bioenergetics may contribute to the onset and progression of ALS/FTD. Here we sought to investigate the pathophysiological signatures of mitochondrial dysfunction associated with ALS/FTD. By means of label-free mass spectrometry (MS) and mRNA sequencing (RNA-seq), we report pre-symptomatic and symptomatic changes in the cortices of TDP-43 and FUS mutant mouse models. Using tissues from transgenic mouse models of mitochondrial diseases as a reference, we performed comparative analyses and extract unique and common mitochondrial signatures that revealed neuroprotective compensatory mechanisms in response to early damage. In this regard, upregulation of both Acyl-CoA Synthetase Long Chain Family Member 3 (ACSL3) and mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) were the most representative change in pre-symptomatic ALS tissues, suggesting that fatty acid beta-oxidation and mitochondrial protein translation are mechanisms of adaptation in response to ALS pathology. Mechanistically, we demonstrate that downregulation of ACS-4/ACSL3 and YARS-2/YARS2 was sufficient to influence mitochondrial bioenergetics and to induce proteotoxicity in the nematode Caenorhabditis elegans. Together, our unbiased integrative analyses unveil novel molecular components that may influence mitochondrial homeostasis in the earliest phase of ALS.