Variants within the mitochondrial genome (mtDNA) disrupt organelle function and lead to severe multi-system disease. mtDNA partitioning in complex tissues has implications for how cellular dosing of genetic variants governs pathogenesis. Here, we profiled the transcriptome, chromatin accessibility state, and heteroplasmy of the most common pathogenic mitochondrial mutation, m.3243A>G, in single cells from the retina and choroid of a patient with retinal and systemic disease. We found that the proportion of the pathogenic m.3243G allele was neither evenly nor randomly distributed across ocular cell types. All classes of cells in the neural retinal exhibited a high percentage of the mutant variant. However, endothelial and lymphocyte populations of the choroid were near homoplasmic for the wildtype allele. Gene expression analysis revealed that the presence of m.3243G deranges expression and causes upregulation of MTRNR2L1, a pseudogene of humanin, known to be protective against oxidative damage. We further found by joint multimodal sequencing of the retinal pigment epithelium that a high proportion of 3243G variant was associated with transcriptionally and morphologically abnormal cells. Together, these findings illuminate the non-random nature of mitochondrial variant partitioning and demonstrate that m.3243A>G causes non-cell autonomous dysfunction in the complex and metabolically linked light-sensing tissue of the eye.