Background <p>Arctic warming is driving uneven greening across high-latitude regions, leading to the development of unusually productive tundra ecosystems that remain poorly understood. Here, we investigated the soil physicochemical properties and multi-kingdom microbial communities (bacteria, fungi, and micro-eukaryotes) in the rhizosphere of dominant plant species in a highly productive tundra ecosystem in the central part of North Greenland (above 82°N).</p> Results <p>A strong correlation between the normalized difference vegetation index (NDVI) and soil moisture content underscores the critical role of moisture in determining vegetation patterns. Plant species was a key determinant of microbial community structure across all microbial groups, but the strength and nature of these associations varied. Fungal communities were most affected by plant species identity, with distinct associations between mycorrhizal taxa and specific plant species observed in wetter sites. In contrast, bacterial communities were more strongly linked to vegetation-driven changes in soil geochemistry, while micro-eukaryotic communities exhibited comparatively weaker responses to both plant species and soil properties. Additionally, a positive association between nematodes and mushroom-forming fungi (mainly <i>Agaricomycetes</i>) suggests the presence of a functionally interconnected soil food web, and parasitic protists of the <i>Apicomplexan</i> order <i>Eugregarinorida</i> were widespread across most sites, though their ecological roles remain unclear.</p> Conclusions <p>Taken together, our findings suggest a possible role of soil water availability in shaping plant species-specific rhizosphere microbial communities in this highly productive High Arctic tundra ecosystem. Furthermore, the multi-kingdom community data provide a valuable baseline for future research on the ecological functioning and climate sensitivity of increasingly productive Arctic ecosystems.</p>