Protein quality control pathways have evolved to ensure the fidelity of protein synthesis and efficient clearance of potentially toxic species. Defects in ribosome-associated quality control (RQC) have been implicated in the accumulation of aberrant proteins and neurodegeneration. The C9orf72 repeat expansion is the most prevalent pathogenic variant of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). C9orf72 repeat-associated non-AUG translation has been suggested to involve inefficient translation elongation, causing ribosomal pausing, and activation of RQC pathways. However, the role of the RQC complex in the processing of proteins generated through this non-canonical translation is not well-understood. We used reporter constructs for a canonical RQC substrate, non-STOP mRNA, to further characterize the role of the RQC in the clearance of aberrant proteins. In addition, we utilized reporters containing the C9orf72-repeat, RQC complex deficient cell models and stain for RQC markers in C9orf72-expansion carrier human tissue to understand its role in dipeptide repeat protein (DPR) pathology. We showed that the non-STOP mRNA products are efficiently cleared by the canonical RQC complex in mammalian cells. Furthermore, we show that the C9orf72-associated repeats induce ribosome stalling when arginine (R)-rich DPR proteins are synthesized. However, despite triggering this pathway, these R-rich DPR proteins are not efficiently processed by the core components of the RQC complex (listerin, nuclear export mediator factor (NEMF) and valosin-containing protein (VCP)) partly due to lack of lysine residues which precludes ubiquitination. Deficient processing by this complex and impaired RQC function may be implicated in C9orf72-expansion associated disease as DPR inclusions were observed to be predominantly devoid of ubiquitin and co-accumulate with NEMF in frontal cortex and cerebellum tissue of mutation carriers. Moreover, evidence of co-aggregation of poly-PR with proteasomal subunits and impairment of this downstream protein degradation machinery may further contribute to dysfunction. These findings suggest that impaired processing of R-rich DPR proteins derived from repeat-associated non-AUG translation by the RQC complex may contribute to protein homeostasis dysregulation observed in C9orf72-expansion ALS and FTD neuropathogenesis.