Life history traits determine the persistence and reproduction of each species. Factors that can affect life history traits are numerous and can be of different origin. We investigated the influence of population origin and heavy metal exposure on microbiota diversity and two life history traits, egg-to-adult viability and developmental time, in Drosophila melanogaster and Drosophila subobscura, grown in the laboratory on a lead (II) acetate-saturated substrate. We used 24 samples, 8 larval and 16 adult samples (two species × two substrates × two populations × two sexes). The composition of microbiota was determined by sequencing (NGS) of the V3–V4 variable regions of the 16S rRNA gene. The population origin showed a significant influence on life history traits, though each trait in the two species was affected differentially. Reduced viability in D. melanogaster could be a cost of fast development, decrease in Lactobacillus abundance and the presence of Wolbachia. The heavy metal exposure in D. subobscura caused shifts in developmental time but maintained the egg-to-adult viability at a similar level. Microbiota diversity indicated that the Komagataeibacter could be a valuable member of D. subobscura microbiota in overcoming the environmental stress. Research on the impact of microbiota on the adaptive response to heavy metals and consequently the potential tradeoffs among different life history traits is of great importance in evolutionary research.