The effect of logging on atmospheric carbon concentrations remains highly contested, especially in the tropics where it is associated to forest degradation. To contribute to this discussion, we estimated the carbon balance from logging natural tropical forests in Costa Rica through a life cycle accounting approach. Our system included all major life cycle processes at a regional level during one rotation period (15 years). We used mass flow analysis to trace biogenic carbon. Data were gathered from all logging operations in the Costa Rican NW region (107 management plants), a sample of industries transforming wood into final products (20 sawmills), and national reports. We estimated a surplus of −3.06 Mg C ha−1 15 year−1 stored within the system. When accounting for uncertainty and variability in a Monte Carlo analysis, the average balance shifted to −2.19 Mg C ha−1 15 year−1 with a 95% CI of −5.26 to 1.86. This confidence interval reveals probabilities of a net increase in atmospheric carbon due to harvesting although these are smaller than those from a system that acts as a reservoir. Our results provide evidence for the carbon neutrality of bio-materials obtained from natural forests. We found that anthropogenic reservoirs play a determinant role in delaying carbon emissions and that these may explain differences with previous carbon balance studies on tropical forest management. Therefore, the climate mitigation potential of forest-derived products is not exclusive to forest management, but measures should be considered throughout the processes of wood transformation, use, and disposal.