Despite the low timber productivity of Mediterranean Pinus halepensis Mill. forests in south-eastern Spain, they are a valuable carbon sequestration source which could be extended if young stands and understories were considered. We monitored changes in biomass storage of young Aleppo pine stands naturally regenerated after wildfires, with a diachronic approach from 5 to 16 years old, including pine and understory strata, at two different quality sites (dry and semiarid climates). At each site, we set 21 permanent plots and carried out different thinning intensities at two ages, 5 and 10 years after fires. We found similar post-fire regeneration capacity at both sites in terms of total above-ground biomass storage ~6 Mg ha−1 (3 Mg ha−1 of the above-ground pine biomass plus 3 Mg ha−1 of the above-ground understory biomass), but with a contrasting pine layer structure. Generally, across the diachronic study, the earlier thinning reduced biomass stocks at both sites, except for the best quality site (the dry site), where the earliest thinning (applied at post-fire year 5) enlarged carbon storage by 11 % as compared to non-thinned plots. We found root:shoot ratios of an average 0.37 for the pine layer and 0.45 for the understory layer. These results provided new information which not only furthers our understanding of carbon sequestration in low timber productivity Mediterranean forests, but will also help to develop new guidelines for sustainable management adapted to the high-risk terrestrial carbon losses of fire-prone areas.