To understand carbon (C) decomposition under cyclic, time-varying oxygen (O2) fluctuations, we incubated two disparate soils (Oxisol and Mollisol) under five fluctuating oxygen treatments (0, 2, 4, 8, or 12 days of anoxic conditions followed by 4 days of oxic conditions), and measured C decomposition as CO2 and CH4 (and their stable isotope compostion) at 2–4-day measurement timesteps for 384 days. We also used a process-based mechanistic model to test C decomposition in response to O2 fluctuations. This dataset supports the findings described in the associated manuscript by Huang et al. (2021).