Microorganisms not only exist at spatial scales that are orders of magnitude smaller than that of ecosystems, but microbial activities occupy timescales of minutes versus the decades required for ecosystem development. Nevertheless, microorganisms affect the long-term dynamics of ecosystems through their impact on soil carbon cycling and sequestration. In particular, the microbial role in the genesis versus turnover of slow carbon pools may be critical in determining ecosystem response to global-scale changes in climate. Here I address the question of how microbial response to environmental stressors (such as temperature) can determine or constrain carbon cycling and response to soil warming. Over short timescales microbial response to soil warming results in accelerated turnover of labile carbon pools. As readily available substrates are exhausted, and in response to increased temperatures, both microbial community composition and carbon utilization patterns will change. Eventually, microbial response to temperature stress and decreased substrate availability can impact the production and turnover of recalcitrant carbon pools. The long-term response of an ecosystem to soil warming ultimately becomes a function of this microbial ecophysiological response and corresponding role in stable carbon genesis and turnover.