Inbreeding depression is a key factor in the evolution of mating strategies and breeding systems across the eukaryotic tree of life. Yet its potential impact in partially asexual species has only received little attention. We studied inbreeding depression in the cyclical parthenogen Daphnia magna by following mixtures of inbred and outbred genotypes from an early embryonic stage through hatching to adulthood and then across several asexual generations. We found that, across asexual generations, the frequency of inbred genotypes strongly and constantly decreased, until the experimental populations were almost entirely made up of outbred genotypes. The resulting estimate of inbreeding depression across the entire life cycle was almost 100 %, much higher than previous estimates for this and other similar species. Our results illustrate that the magnitude of inbreeding depression may be severely underestimated in studies that use fitness components or proxies instead of compound fitness estimates across the entire life, as well as in experimental studies with substantial pre-experimental mortality. More generally, our results suggest that inbreeding depression may play an important role in the evolution of partially asexual life cycles because clonal reproduction maintains inbreeding levels, and hence the negative effects of inbreeding accumulate across subsequent asexual generations.