Alterations to mitochondrial function and mutations in mitochondrial genes have been reported for a wide variety of cancers, however the mitochondrial transcriptome remains largely unexplored in cancer despite an emerging appreciation of the role that post-transcriptional regulation plays in the etiology of these diseases. Here, we quantify and assess changes to mitochondrial RNA processing in human cancers using integrated genomic analysis of RNA Sequencing and genotyping data from 1226 samples across 12 different cancer types. We find significant changes to m1A and m1G post-transcriptional methylation rates at functionally important positions in mitochondrial tRNAs in tumor tissues across all cancers. Pathways of RNA processing are strongly associated with methylation rates in normal tissues (P=2.85x10-27), yet these associations are lost in tumors. Furthermore, we report 18 gene-by-disease-state interactions where altered methylation rates occur under cancer status conditional on genotype, implicating genes associated with mitochondrial function or cancer (e.g. CACNA2D2, LMO2 and FLT3) and suggesting that nuclear genetic variation can potentially modulate an individual's ability to maintain unaltered rates of mitochondrial RNA processing under cancer status. Finally, we report a significant association between the magnitude of methylation rate changes in tumors and patient survival outcomes. These results highlight mitochondrial post-transcriptional events as a clinically relevant mechanism and as a theme for the further investigation of cancer processes, biomarkers and therapeutic interventions.