Significance R loops form during transcription when the mRNA hybridizes back to the template DNA forming a stable DNA–RNA hybrid. Stable R loops can block replication and transcription machineries, leading to genome instability and human diseases. We report that the human mitochondrial degradosome (mtEXO), formed by SUV3 and PNPase, plays an important role in R-loop metabolism in the mitochondria apart from preventing dsRNA accumulation, with implications in replication and preventing instability of the mitochondrial genome. Our findings help establish a connection between the RNA processing activities of the mtEXO and mitochondrial genome stability, affecting mitochondria homeostasis, cellular metabolism, and human diseases.