Nutrition fuels any activity performed by an organism and has been shown to affect its ability to withstand pathogens and parasites. Furthermore, animals over a wide range of taxa have been shown to exhibit a choice of foods and nutrients that are beneficial to their fitness. Saprophagous animals most often feed on microorganisms growing on dead organic matter rather than the organic matter itself. Various yeast species play an important role in both larval and adult nutrition of saprophagous Drosophila melanogaster. We hypothesised the dietary microbial species to affect life‐history traits of D. melanogaster, including the ability to fend offparasitoids, and larvae to prefer to devour those yeast species beneficial to their development and immunocompetence. Particular yeast species known to be associated with D. melanogaster could be shown to have a substantial influence on various larval and adult fitness traits including the ability to encapsulate eggs of the parasitoid wasp Asobara tabida. It also turned out that larvae chose to devour those yeast species which supported their ability to encapsulate parasitoid eggs. Which yeast species was preferred and had a beneficial impact on encapsulation ability, was subject to inter‐individual variability within the investigated population, hinting at the existence of an adaptive heritable variability regarding individual choice and salubriousness of food. The results suggest that the dietary microbial species of saprophagous insects may influence the resistance against parasitoid attacks and thus the outcome of the interaction between a saprophagous host and its parasitoids.