Ecosystem carbon flux partitioning is strongly influenced by poorly constrained soil CO2 efflux (Fsoil). Simple model applications (Arrhenius and Q10) do not account for observed diel hysteresis between Fsoil and soil temperature. How this hysteresis emerges and how it will respond to variation in vegetation or soil moisture remains unknown. We used an ecosystem-level experimental system to independently control potential abiotic and biotic drivers of the Fsoil-T hysteresis. We hypothesized a principally biological cause for the hysteresis. Alternatively, Fsoil hysteresis is primarily driven by thermal convection through the soil profile. We conducted experiments under normal, fluctuating diurnal soil temperatures and under conditions where we held soil temperature near constant. We found (i) significant and nearly equal amplitudes of hysteresis regardless of soil temperature regime, and (ii) the amplitude of hysteresis was most closely tied to baseline rates of Fsoil, which were mostly driven by photosynthetic rates. Together, these findings suggest a more biologically-driven mechanism associated with photosynthate transport in yielding the observed patterns of soil CO2 efflux being out of sync with soil temperature. These findings should be considered on future partitioning models of ecosystem respiration.