Climate change significantly affects peatland ecosystems, which are among the most sensitive and endangered in Europe. Carnivorous plants, such as Utricularia vulgaris together with their associated microbial communities, are integral components of these habitats. This study aimed to investigate how increasing water temperature influences the abundance, biomass, and diversity of microorganisms living both in the water and inside plant traps, in two contrasting peatland types: a Sphagnum peat bog and a carbonate-rich fen. The research demonstrated that microbial communities are more abundant and diverse in water than in plant traps. Elevated temperatures generally stimulated microbial growth, especially in habitats with a higher trophic status; however, such conditions negatively affected the microbiome within the plant traps. The results suggest that the microbiome of Utricularia vulgaris traps reflects the fertility of the surrounding environment. These findings are crucial for understanding how global warming may alter the delicate balance of peatland ecosystems and their biodiversity. This knowledge is valuable for future conservation efforts, as it identifies early bioindicators of climate change and informs strategies to protect vulnerable wetland species and their habitats.