Global climate change and increasing human impact are the main factors intensifying eutrophication of peatland ecosystems. Due to the high sensitivity of certain groups of microorganisms, they can serve as indicators of the degree of eutrophication and thereby provide much important information for assessment of the state of peatland ecosystems. However, there is still little knowledge of how changes in the fertility of the environment can affect the microbiome of carnivorous plants in these ecosystems. This study was conducted to verify the following hypotheses: (1) the microbiome of carnivorous plant traps reflects the trophic status of the habitat; (2) an increase in the concentration of biogenic compounds causes a greater increase in the size of microbial communities in the aquatic environment than in the traps. An experiment was carried out in laboratory conditions to determine the effect of simulated eutrophication on the microbiome of Utricularia vulgaris L. An experimental increase in habitat fertility caused an increase in the abundance of bacteria, flagellates, testate amoebae, ciliates, and rotifers, while a decrease in abundance was observed for crustaceans. The increase in the concentration of biogenic compounds also modified the taxonomic composition of communities of microorganisms and small metazoa as well as the strength of trophic relationships; as the trophic level increased, the relationships between bacteria and heterotrophic flagellates; bacteria and testate amoebae; and bacteria and ciliates became stronger.