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Global warming is expected to significantly impact the soil fungal and bacterial microbiomes, yet the predominant ecological response of microbial taxa—whether an increase, decrease, or no change—remains unclear. It is also unknown whether microbial taxa from different evolutionary lineages exhibit common patterns and what factors drive these changes. Here, we analyzed three mid‐term (> 5 years) warming experiments across contrasting dryland and temperate‐boreal ecosystems, encompassing over 500 topsoil samples collected across multiple time points. We found that warming altered the relative abundance of microbial taxa, with both increases and decreases over time. For instance, the relative abundance of bacterial and fungal taxa responding to warming (increase or decrease) accounted for 35.9% and 42.9% in the dryland ecosystem, respectively. Notably, taxa within the same phylum exhibited divergent responses to warming. These ecological shifts were linked to factors such as photosynthetic cover and fungal lifestyle, both of which influence soil functions. Overall, our findings indicate that soil warming can reshape a significant fraction of the microbial community across ecosystems, potentially driving changes in soil functions.