The CO2/O2 fluxes ratio (apparent respiration quotient [ARQ]) measured in soils and plants contains valuable information about the respiratory-substrate stoichiometry and biotic and abiotic non-respiratory processes. We investigated ARQ variability by measurements in soil pore space air, and in headspace air from incubations of bulk-soil and tree stem tissues (both fresh and 24-hr stored tissues) in 10 measurement campaigns over 15 months in a Mediterranean oak forest. Mean (range) ARQ values were: soil air, 0.76 (0.60–0.92); bulk soil, 0.75 (0.53–0.90); fresh stem tissues, 0.39 (0.19–0.70); and stored stem tissues, 0.68 (0.42–1.08). The variability in tree stems was assumed to be controlled by CO2 re-fixation that lowered ARQ from 1.0, the value expected for carbohydrate respiration in plants. We estimate that the values of the stored tissues represent better stem metabolism since the fresh-tissue results contained a signal of wound-response O2 uptake that further lowered ARQ. The mean bulk-soil ARQ (0.75) was considerably lower than expected by soil organic matter (SOM) stoichiometry (0.95). This lower value might represent the stoichiometry of the SOM sub-pool that supports respiration, and/or oxidative depolymerization that increases O2 fluxes. Abiotic O2 uptake was demonstrated to reduce bulk-soil ARQ down to 0.37 and consume Fe2+, but estimated to have small effect under typical respiration rates. Soil-air ARQ was usually higher than bulk-soil ARQ and lower than root ARQ (which, when measured, ranged from 0.73 to 0.96), demonstrating the potential of ARQ to partition the autotrophic and heterotrophic sources of soil respiration. The limitations of this partitioning method are discussed.