Understanding soil respiration (SR) dynamics is essential for predicting climate change impacts on terrestrial carbon cycles. However, there is limited knowledge about how microbial community composition and metabolic state affect SR in mountainous areas, where environmental conditions are highly variable and warming occurs faster than in other regions. This study examines the relationship between SR and microbial (ITS- and 16S-based) gene copy numbers from intracellular DNA (iDNA) in alpine and subalpine grassland soils. By focusing on iDNA, we exclude non-organismic extracellular DNA and analyze DNA from intact cells, whether active or dormant. We calculate a gene-copy specific respiration rate (GSRR) and categorize microbial communities into different metabolic states. Our findings show a positive correlation between GSRR and Q10, with highly active microbial communities found at lower elevations with higher inclinations, more favorable pH, and C:N ratios. Additionally, greater soil fauna richness and diversity reduced microbial activity levels, while prokaryote richness and diversity were highest in the most active and most dormant communities. This study provides new insights into the relationships between microbial metabolic states and SR in alpine and subalpine grasslands, enhancing our understanding of these complex interactions and the effects of global warming on terrestrial carbon cycles.