Timber harvests remove a significant portion of ecosystem carbon. While some of the wood products moved off-site may last past the harvest cycle of the particular forest crop, the effect of the episodic disturbances on long-term on-site carbon sequestration is unclear. The current study presents a 25 year carbon budget estimate for a typical commercial loblolly pine plantation in North Carolina, USA, spanning the entire rotation cycle. We use a chronosequence approach, based on 5 years of data from two adjacent loblolly pine plantations. We found that while the ecosystem is very productive (GEP up to 2900 g m−2 yr−1, NEE at maturity about 900 g C m−2 yr−1), the production of detritus does not offset the loss of soil C through heterotrophic respiration (RH) on an annual basis. The input of dead roots at harvest may offset the losses, but there remain significant uncertainties about both the size and decomposition dynamics of this pool. The pulse of detritus produced at harvest resulted in a more than 60% increase in RH. Contrary to expectations, the peak of RH in relation to soil respiration (SR) did not occur immediately after the harvest disturbance, but in years 3 and 4, suggesting that a pool of roots may have remained alive for the first few years. On the other hand, the pulse of aboveground RH from coarse woody debris lasted only 2 years. The postharvest increase in RH was offset by a decrease in autotrophic respiration such that the total ecosystem respiration changed little. The observed flux rates show that even though the soil C pool may not necessarily decrease in the long-term, old soil C is definitely an active component in the site C cycle, contributing about 25–30% of the RH over the rotation cycle.