Forests exchange CO and O with the atmosphere at similar molar ratios. Correspondingly, the apparent respiratory quotient (CO/O flux ratio, ARQ) is expected to be ≈1 given the stoichiometry of organic substrates in soils and plants. However, measured ARQ values often deviate from ≈1, and it is still unclear how CO and O fluxes are balanced among ecosystem components, and what are the sources of ARQ variability. Here we measured ARQ of soil pore space air (ARQ), and in headspace air from incubations of bulk-soil (ARQ), tree stem-cores (ARQ) and roots in 10 measurement campaigns over 15 months in a Mediterranean oak forest. Mean (range) values were: ARQ = 0.76 (0.60-0.92), ARQ = 0.75 (0.53-0.90), and ARQ = 0.39 (0.19-0.70). As expected, ARQ was usually higher than ARQ and lower than the ARQ of incubated roots (range of 0.73-0.96). Variability in ARQ was correlated with soil moisture parameters. Temperature positively correlated with ARQ and ARQoutside the growing season. Abiotic O uptake by Fe was demonstrated to reduce ARQ, but this effect would be significant under field conditions only if respiration rates are very low. We hypothesize that low measured ARQ values likely result from selective decomposition of reduced compounds and physical protection of oxidized compounds. ARQ, measured at two stem positions, was lower than expected from oxidation of any possible substrate, indicating partial retention of respired C. The overall ARQ <1 reveals an imbalance of stem-soil CO and O fluxes that is unexpected at the ecosystem level.