Background and aims <p>Climate warming can lead to changes in plant functional types (PFTs) in permafrost peatlands, which can subsequently affect soil properties and microbial functional structures. Although the effects of PFTs changes on soil microorganisms in various ecosystems have been documented, these effects are not well understood in permafrost peatlands.</p> Methods <p>This study investigated the impact of removing different PFTs (sedges, evergreen shrubs, deciduous shrubs, and mosses) on soil properties and microbial functional structures (microbial activity, microbial diversity, and carbon source utilization) in a permafrost peatland.</p> Results <p>Variations in PFTs lead to changes in soil properties and microbial functional structures. Removal of shrubs and mosses increased soil dissolved organic carbon (DOC) content by 26% and inorganic nitrogen content by 28%, the soil microbial activity and diversity were significantly enhanced, and microbes preferred amino acids and carboxylic acids as carbon sources compared to the natural control (N). In contrast, the moss treatment (M) with shrubs and sedge removed had 30% lower soil DOC and 50% lower inorganic nitrogen content, as well as a significant reduction in microbial activity and diversity, with microorganisms preferring to utilize polymers as a carbon source.</p> Conclusion <p>These results indicate that peatland microorganisms are sensitive to changes in PFTs over short time scales, with a particularly rapid response to specific plant functional groups such as sedges. These findings highlight the critical role of PFTs as drivers of microbial functional structures and suggest that future vascular plant expansion may alter peatland microbial functional structures and carbon cycling in the context of climate change.</p>