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Defaunation including invertebrate decline is one of the major consequences of anthropogenic alterations of the environment. Despite recent reports of ubiquitous invertebrate decline, the ecosystem consequences have been rarely documented. We exposed standardized plant communities grown in the iDiv Ecotron to different levels of invertebrate numbers and biomass and tracked effects on the diversity and composition of bacterial communities associated with flowers and leaves of Scorzoneroides autumnalis and Trifolium pratense using next-generation 16S rRNA gene amplicon sequencing. Our data indicate that invertebrate decline reduces bacterial richness and β-diversity and alters community composition. These effects may result from direct effects of invertebrates that may serve as dispersal agents of bacteria; or from indirect effects where animal-induced changes in the plant's phenotype shape the niches plants provide for bacterial colonizers. Because bacteria are usually not dispersal limited and because species sorting, i.e. niche-based processes, has been shown to be a dominant process in bacterial community assembly, indirect effects may be more likely. Given that a healthy microbiome is of fundamental importance for the well-being of plants, animals (including humans) and ecosystems, a loss of bacterial diversity may be a dramatic yet previously unknown consequence of current invertebrate decline., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)