Aims <p>Due to climate warming, numerous riparian wetlands are at risk of transitioning from mudflats to vegetated regions. Protists, sensitive to environmental changes, play a crucial role in regulating soil biogeochemical cycling. However, the effect of warming on soil protists during sedge colonization remains poorly understood. Thus, we aimed to investigate how elevated temperatures affect diversity, community composition, and co-occurrence networks of soil protists during sedge colonization.</p> Methods <p>A mesocosm experiment simulated sedge expansion under warming over a full growing season.</p> Results <p>Warming significantly increased protist alpha diversity in mudflats but not in vegetated soils. Moreover, warming increased the network nodes and edges by 42.1% and 55.8% in mudflats. However, warming had minimal effects on ecological networks in vegetated soils, indicating that sedge expansion could weaken warming-driven protist interactions. Warming changed the community composition and structure of protists in both mudflats and vegetated soils. Particularly, relative abundances of Cercozoa and Haptista decreased during sedge colonization. Temperature, NH₄⁺-N, and soil moisture were key regulators in mudflats, while temperature, NO₃⁻-N, plant height, and stem density shaped those in vegetated areas.</p> Conclusions <p>Sedge colonization weakens the impact of climate warming on soil protist communities in riparian wetlands. Although warming significantly increased protist alpha diversity and network complexity in mudflats, these effects were minimal in vegetated areas, suggesting that vegetation cover weakens warming-induced intensification of microbial interactions. These findings will provide theoretical and practical guidance for the early warning, prevention, and management of sedge expansion and the conservation of wetland ecosystems under climate warming.</p>