Insect midgut microbial symbionts have been considered as an integral component in thermal adaptation due to their differential thermal sensitivity. Altered midgut microbial communities can influence both insect physiology and competence for important vector-borne pathogens. This study sought to gain insights into how Aedes aegypti midgut microbes and life history traits are affected by increase in baseline diurnal temperature. Increase in temperature resulted in the enrichment of specific taxa with Bacillus being the most enriched. Bacillus is known to be heat tolerant. It also resulted in a dissimilar microbial assemblage (Bray–Curtis Index, PERMANOVA, F = 2.2063; R2 = 0.16706; P = 0.002) and reduced survivorship (Log-rank [Mantel-Cox] test, Chi-square = 35.66 df = 5, P < 0.0001). Blood meal intake resulted in proliferation of pathogenic bacteria such as Elizabethkingia in the midgut of the mosquitoes. These results suggest that alteration of temperature within realistic parameters such as 2 °C for Ae. aegypti in nature may impact the midgut microbiome favoring specific taxa that could alter mosquito fitness, adaptation and vector–pathogen interactions.