The epidemiological and ecological processes which govern the success of multiple-species co-infections are as yet unresolved. Here we investigated prior versus late residency within hosts, meaning which parasite contacts the host first, to determine if the outcomes of intra-host competition are altered. We infected a single genotype of the waterflea Daphnia galeata with both the intestinal protozoan Caullerya mesnili and the haemolymph fungus Metschnikowia sp. (single genotype of each parasite species), as single infections, simultaneous co-infections and as sequential co-infections, with each parasite given 4 days prior residency. Simultaneous co-infections were significantly more virulent than both single infections and sequential co-infections, as measured by a decreased host life span and fecundity. Further, in addition to the Daphnia host, the parasites also suffered fitness decreases in simultaneous co-infections, as measured by spore production. The sequential co-infections, however, had mixed effects: C. mesnili benefited from prior residency, whereas Metschnikowia sp. experienced a decline in fitness. Our results show that multiple-species co-infections of Daphnia may be more virulent than single infections, and that prior residency does not always provide a competitive advantage.