Many studies have shown that associated microbiota influences the life history traits of Drosophila melanogaster. The increase in bacterial load reduces lifespan but may increase fecundity. Paradoxically, the influence of yeast microbiota, a key food source for fruit flies, on life history traits is much less studied. In this work, we assessed the influence of natural yeast microbiota, as well as individual yeast species, on lifespan, age-related dynamics of fecundity, and mortality in the control fly line and the fly line with depleted yeast microbiota. We used Starmerella bacillaris, Zygosaccharomyces bailii, and Saccharomyces cerevisiae as individual yeast species for testing. We have shown that the decrease in the amount of symbiotic yeast on the medium, on the surface of the body, or in the fly intestine leads to an increase in lifespan and a decrease in fecundity for flies reared on standard medium. It is consistent with the “disposable soma” hypothesis. At the same time, an increase in lifespan does not compensate for the decrease in fecundity; therefore, the decrease in the number of yeasts leads to a decrease in fly fitness. Inoculation of S. cerevisiae on the medium shifts the reproduction of the control flies to an earlier age, while two other yeast species increase fertility significantly. Inoculation of S. bacillaris and S. cerevisiae (not typical for the microbiota of tested fly lines) on the medium reduces lifespan more than yeast Z. bailii, which is typical for the microbiota of the control line. Yeast microbiota reduces the lifespan of the Drosophila males more than the females. The results indicate deep coevolutionary relationships between the components of the yeast microbiota and the host organism, requiring further studies within the hologenome theory of evolution.