Background: Microplastics are a pervasive pollutant widespread in sea- and freshwater from anthropogenic sources, and together with the presence of pesticides, they can have physical and chemical effects on aquatic organisms and on their microbiota. Few studies have explored the combined effects of microplastics and pesticides on the host microbiome, and more importantly, the effects across multiple trophic levels. In this work, we studied the effects of exposure to microplastics and the pesticide deltamethrin on the diversity and abundance of the host microbiome across a three-level food chain: daphnids-damselfly-dragonflies. Daphnids were the only organism exposed to 1µm microplastic beads, and they were fed to damselfly larvae. Those damselfly larvae were exposed to deltamethrin and then fed to the dragonfly larvae. The microbiotas of the daphnids, damselflies, and dragonflies were analyzed. Results: Our results suggest that the exposure to microplastics and deltamethrin had negative carry-over effects on the diversity and abundance of the microbiome across the three trophic levels. Moreover, the exposure to deltamethrin on the damselflies negatively affected their survival rate in the presence of the dragonfly predator, but no such effects were found on damselflies exposed to only microplastics. Conclusions: Our study highlights the importance of evaluating ecotoxicological effects at the community level. Importantly, the indirect exposure to microplastics and pesticides through diet can potentially have bottom-up effects on the trophic webs.