<p>The stability of soil microbiomes is critical for ecosystem functioning under climate change, yet its assessment is confounded by the overlooked problem of observational temporal scale dependency. Here, we introduce a multi-temporal window framework to resolve this problem. Applied to a decade-long warming experiment, our approach reveals that the perceived stability of bacterial and fungal communities nonlinearly decays with observational temporal scale, and short windows systematically overestimate it. Crucially, we document a temporal scale-driven mechanistic shift. Community stability shifts from species resistance to compensatory asynchrony once the window exceeds a threshold. This transition occurs over a broader temporal scale range for fungi than for bacteria. Our work establishes that microbiome stability is an intrinsically temporal scale-dependent property and provides a scalable, bioinformatic-friendly framework that challenges conventional single-temporal-scale assessments. This paradigm is critical for accurately predicting the fate of soil carbon and other microbiome-governed functions in a warming world.</p>