Motor neurons are highly polarized cells in which local translation plays a fundamental role not only in maturation but also in the maintenance of their long axons. One of the earliest events occurring in amyotrophic lateral sclerosis (ALS) is the denervation of the neuromuscular junctions (NMJs), which suggests that local events may be valuable as therapeutic approach. We identified suppression in axonal translation as an early feature of ALS mice expressing the full-length human FUS gene harboring ALS-causing R521H/C mutations, suggesting that disruption of local protein synthesis may underlie the early axonal/NMJ demise observed in ALS. In this project, we aimed to unravel the transcriptional signature of motor neuron cell bodies in the mouse spinal cord and their respective axons in the adult sciatic nerves in healthy and mutant FUS animals for the identification of early molecular players in the maintenance of mature axons and their dysregulation in ALS. Cutting-edge spatial transcriptomics approaches, including untargeted barcoded and targeted multiplexed single molecule fluorescence in situ hybridization technologies, were used on 12-months old mouse spinal cord and sciatic nerve sections. Using a combination of in vivo immunofluorescence imaging and subsequent validation with compartmentalized microfluidic devices for the in vitro separation of cell bodies and axons, newly identified targets were validated and further investigated for their role in ALS pathogenesis. We discovered that FUS mutation disrupts the compartment-specific RNA signatures including components of the translation machinery. In particular, an eukaryotic initiation factor, critical for protein synthesis regulation, is found to be locally impaired in axons. Using an axon-specific treatment targeting its activation, we show rescue of the local translation defects provoked by ALS-causing FUS mutation in motor axons. Our findings provide critical novel mechanistic insights into compartment-specific toxic pathways that may advance future therapeutic development to treat ALS.