Autosomal dominant mutations in α-synuclein, TDP-43 and tau promote protein aggregation and neurodegeneration. Rates of aggregation are highly dependent on protein concentration, which can be regulated via lysosomal proteolysis. Lysosomal cathepsins recognize specific linear amino acid sequences; thus, mutations in α-synuclein, TDP-43 and tau have the potential to impact protein half-life by impairing lysosomal degradation. To test this, we first generated comprehensive proteolysis maps containing cathepsin cleavage sites for each of these disease-associated proteins. In silico analysis of these maps suggested that certain mutations would diminish cathepsin cleavage, a prediction we validated utilizing in vitro protease assays. We further demonstrated that lysosomes degrade inducibly-expressed mutant forms of α-synuclein, TDP-43 and tau less efficiently than wild-type protein. Together, this study provides evidence that pathogenic mutations in α-synuclein, TDP-43 and tau directly impair their own lysosomal degradation, altering protein homeostasis by increasing the half-life of these proteins.