High latitude warming and permafrost thaw will expose vast stores of deep soil organic carbon (SOC) to decomposition. Thaw also changes water movement causing either wetter or drier soil. The fate of deep SOC under different thaw and moisture conditions is unclear. We measured weekly growing‐season δ13C of ecosystem respiration (Recoδ13C) across thaw and moisture conditions (Shallow‐Dry; Deep‐Dry; Deep‐Wet) in a soil warming manipulation. Deep SOC loss was inferred from known δ13C signatures of plant shoot, root, surface soil, and deep soil respiration. In addition, a 2‐year‐old vegetation removal treatment (No Veg) was used to isolate surface and deep SOC decomposition contributions to Reco. In No Veg, seasonal Recoδ13C indicated that deep SOC loss increased as the soil column thawed, while in vegetated areas, root contributions appeared to dominate Reco. The Recoδ13C differences between Shallow‐Dry and Deep‐Dry were significant but surprisingly small. This most likely suggests that, under dry conditions, soil warming stimulates root and surface SOC respiration with a negative 13C signature that opposes the more positive 13C signal from increased deep SOC respiration. In Deep‐Wet conditions, Recoδ13C suggests reduced deep SOC loss but could also reflect altered diffusion or methane (CH4) dynamics. Together, these results demonstrate that frequent Recoδ13C measurements can detect deep SOC loss and that plants confound the signal. In future studies, soil profile δ13C measurements, vegetation removal across thaw gradients, and isotopic effects of CH4 dynamics could further deconvolute deep SOC loss via surface Reco.