Most multicellular organisms reproduce sexually despite the costs associated with sexuality. This has been explained as the result of selection favouring the ability to recombine the genome. The lack of recombination in asexual species constrains their adaptability and leads to the accumulation of deleterious mutations, ultimately increasing their risk of extinction. Nonetheless, successful asexual life histories persist among multicellular organisms, and explanatory mechanisms which may help limit the cost of asexuality remain enigmatic. In search of these mechanisms, we looked at that the molecular evolutionary changes in sexual and obligate asexual strains of the planarian flatworm, Schmidtea mediterranea. We find that the accumulation of deleterious mutations is largely avoided in the asexual strain. We find evidence that this is achieved by somatic gene conversion in stem cells allowing for the restoration of fit alleles and the purification of deleterious mutations. Our analyses provide a potential mechanism for the maintenance of asexuality in a metazoan. Taken together, these findings suggest that gene conversion may be used by asexual lineages to unlink loci, counteracting some of the key challenges facing obligate asexual species.