Carbon cycling responses of ecosystems to global warming will likely be stronger in cold ecosystems where many processes are temperature‐limited. Predicting these effects is difficult because air and soil temperatures will not change in concert, and will affect above and belowground processes differently. We disentangled above and belowground temperature effects on plant C allocation and deposition of plant C in soils by independently manipulating air and soil temperatures in microcosms planted with either Leucanthemopsis alpina or Pinus mugo seedlings. Daily average temperatures of 4 or 9°C were applied to shoots and independently to roots, and plants pulse‐labelled with ¹⁴CO₂. We traced soil CO₂ and ¹⁴CO₂ evolution for 4 days, after which microcosms were destructively harvested and ¹⁴C quantified in plant and soil fractions. In microcosms with L. alpina, net ¹⁴C uptake was higher at 9°C than at 4°C soil temperature, and this difference was independent of air temperature. In warmer soils, more C was allocated to roots at greater soil depth, with no effect of air temperature. In P. mugo microcosms, assimilate partitioning to roots increased with air temperature, but only when soils were at 9°C. Higher soil temperatures also increased the mean soil depth at which ¹⁴C was allocated. Our findings highlight the dependence of C uptake, use, and partitioning on both air and soil temperature, with the latter being relatively more important. The strong temperature‐sensitivity of C assimilate use in the roots and rhizosphere supports the hypothesis that cold limitation on C uptake is primarily mediated by reduced sink strength in the roots. We conclude that variations in soil rather than air temperature are going to drive plant responses to warming in cold environments, with potentially large changes in C cycling due to enhanced transfer of plant‐derived C to soils.