Several incurable neurodegenerative diseases including motor neuron disease (MND)/amyotrophic lateral sclerosis (ALS) are characterised neuropathologically by accumulation of the normally nuclear RNA-binding protein TDP-43 in the cytoplasm of neurons of affected brain and spinal cord regions. TDP-43 is primarily degraded via the ubiquitin-proteasome system, however pathological forms become aggregated and can be targeted for clearance by macroautophagy. TDP-43-related neurodegenerative diseases are also associated with dysfunction of the autophagy-lysosome pathway. To understand disease processes, we recently completed a longitudinal quantitative proteomics analysis of the brains of transgenic rNLS8 TDP-43 mice (1), which inducibly express cytoplasmic human TDP-43 in neurons of the brain and spinal cord and develop disease phenotypes reminiscent of ALS (2). Within a network of disease-relevant changes occurring across time, protein degradation pathways including components of lysosomal and autophagy systems were altered in abundance, correlating with TDP-43 pathology. Here, we therefore analysed localization and abundance of lysosome-related proteins in rNLS8 TDP-43 mouse cortex and human ALS motor cortex samples using highly multiplexed immunohistochemistry. Further, we developed a blood-brain barrier-crossing adeno-associated virus (AAV) approach to label and purify lysosomes specifically from neurons of the central nervous system of adult mice, and used quantitative mass spectrometry to analyse neuronal lysosome protein abundance alterations in rNLS8 TDP-43 mice. We identified changes in abundance of lysosomal proteins including cathepsin-D and changes in distribution of degradative organelles including lysosomes in neurons, in the rNLS8 mouse motor cortex from early disease stages. Similar changes in lysosome distribution were apparent in neurons of the motor cortex from people with ALS. rNLS8 TDP-43 mouse cortex lysosomes showed alterations in abundance of proteins involved in organelle fusion and enrichment for synaptic and cytoskeletal proteins, amongst thousands of proteins quantified, indicating biological pathways changed in disease. These findings delineate how lysosome-autophagosome function contributes and responds to TDP-43-mediated neurodegeneration.