Recombination via short repeats in plant mitochondrial genomes results in sublimons--DNA molecules with a copy number much lower compared to the main mitochondrial genome. Coexistence of stoichiometrically different mitotypes, called heteroplasmy, plays an important evolutionary role, since sublimons occasionally replace the main genome resulting in a new plant phenotype. It is not clear, how frequency of recombination and sublimon production is regulated and how it is related to changes in the quantity of the main genome and sublimons. We analyzed the accumulation of two recombining main genome sequences and two resulting sublimons in apical meristems, undifferentiated tissues and leaves of different age of Phaseolus vulgaris. Copy numbers of the main genome sequences varied greatly depending on tissue type and organ age while accumulation of sublimons remained much more stable. Although the overall accumulation of plant mtDNA decreased with the leaf age, the quantity of sublimons increased relative to the main genome indicating a higher frequency of recombination via the short 314 bp repeat. Recombination was symmetrical in young developing leaves while in senescent tissues it shifted towards asymmetric events resulting in overrepresentation of one product. We propose that during plant lifetime replication and recombination frequencies change oppositely sustaining heteroplasmic compositions of the genome, which are favorable for inheritance and maintenance of complex plant mtDNA.