This study aims to assess the effects of corrections for disturbances such as an increased amount of dead roots and an increase in volumetric soil water content on the calculation of soil CO2 efflux partitioning. Soil CO2 efflux, soil temperature and superficial soil water content were monitored in two young beech sites (H1 and H2) during a trenching experiment. Trenching induced a significant input of dead root mass that participated in soil CO2 efflux and reduced the soil dissolved organic carbon content, while it increased superficial soil water content within the trenched plot. Annual soil CO2 efflux in control plots was 528 g C m−2 year−1 at H1 and 527 g C m−2 year−1 at H2. The annual soil CO2 efflux in trenched plots was 353 g C m−2 year−1 at H1 and 425 g C m−2 year−1 at H2. By taking into account annual CO2 efflux from decaying trenched roots, the autotrophic contribution to total soil CO2 efflux reached 69% at H1 and 54% at H2. The partitioning calculation was highly sensitive to the initial root mass estimated within the trenched plots. Uncertainties in the remaining root mass, the fraction of root C that is incorporated into soil organic matter during root decomposition, and the root decomposition rate constant had a limited impact on the partitioning calculation. Corrections for differences in superficial soil water content had a significant impact on annual respired CO2 despite a limited effect on partitioning.