Extensive research has focused on comparing the impacts of post-fire salvage logging versus those of less aggressive management practices on forest regeneration. However, few studies have addressed the effects of different burnt-wood management options on seedling/sapling performance, or the ecophysiological mechanisms underlying differences among treatments. In this study, we experimentally assess the effects of post-fire management of the burnt wood on the growth and performance of naturally regenerating pine seedlings (Pinus pinaster). Three post-fire management treatments varying in degree of intervention were implemented seven months after a high-severity wildfire burned Mediterranean pine forests in the Sierra Nevada, southeast Spain: (a) “No Intervention” (NI, all burnt trees left standing); (b) “Partial Cut plus Lopping” (PCL, felling most of the burnt trees, cutting off branches, and leaving all the biomass on site without mastication); and (c) “Salvage Logging” (SL, felling the burnt trees, piling up the logs and masticating the fine woody debris). Three years after the fire, the growth, foliar nutrient concentrations, and leaf carbon, nitrogen and oxygen isotopic composition (δ¹³C, δ¹⁸O and δ¹⁵N) of naturally regenerating seedlings were measured in all the treatments. Pine seedlings showed greatest vigor and size in the PCL treatment, whereas growth was poorest in SL. The nutrient concentrations were similar among treatments, although greater growth in the two treatments with residual wood present indicated higher plant uptake. Seedlings in the SL treatment showed high leaf δ¹³C and δ¹⁸O values indicating severe water stress, in contrast to significantly alleviated water stress indications in the PCL treatment. Seedling growth and physiological performance in NI was intermediate between that of PCL and SL. After six growing seasons, P. pinaster saplings in PCL showed greater growth and cone production than SL saplings. In summary, salvage logging has a detrimental effect on the ecophysiological performance and growth of naturally regenerating pine seedlings, compared to alternative post-fire management practices in which burnt logs and branches are left in situ. Improved seedling growth and performance is associated with the amelioration of microsite/microclimate conditions by the presence of residual burnt wood, which alleviates seedling drought stress and improves nutrient availability through the decomposition of woody debris.