Pathogenic mitochondrial (mt)DNA single nucleotide variants are the most common cause of adult mitochondrial disease. Whilst levels of the most common heteroplasmic variant (m.3243A>G) remain stable in post-mitotic tissues, levels in mitotic tissues, such as blood, decrease with age. Given differing division rates, longevity and energetic requirements within haematopoietic lineages, we hypothesised that variant level decline is driven by cell-type specific mitochondrial metabolic requirements. To address this, we coupled cell sorting with mtDNA sequencing to investigate mtDNA variant levels within progenitor, myeloid and lymphoid lineages from 26 individuals harbouring pathogenic mtDNA variants. We report that whilst the level of m.3243A>G declines with age in all analysed cell types, the T-cell lineage shows a significantly greater decline. This was confirmed for a second pathogenic tRNA variant; m.8344A>G, indicating that this phenomenon is not limited to m.3243A>G. High-throughput single cell analysis revealed that decline is driven by increasing proportions of cells that have cleared the variant genome, following a hierarchy that follows the current orthodoxy of T-cell differentiation and maturation. This work identifies the unique ability of T-cell subtypes to selectively purify their mitochondrial genomes, and identifies pathogenic mtDNA variants as a new means to track blood cell differentiation status.