The majority of tropical forests in the world have undergone or are still undergoing selective logging. This human disturbance is among the actions that most affect the dynamics of the carbon stocks of tropical forests and also the vegetation structure, richness, and species composition. One of the most widely used approaches to understand forest responses to this disturbance has been to compare them with other undisturbed forests in the given region. Here, we measure the effects of the selective logging history on the aboveground biomass, tree abundance, basal area, and wood density in four Brazilian Atlantic Forest fragments logged once, 35–45 years before the current sampling. We used two unlogged forest fragments as reference ecosystems. We found 40% less aboveground biomass (AGB) and 31% lower basal area in logged than in unlogged forest fragments. Large trees (trees with a diameter greater than 50 cm) were strongly affected by selective logging, showing AGB, basal area, mean wood density and tree abundance values 59%, 52%, and 46%, respectively, lower in logged forest fragments. We found an increase in the abundance of softwood, early-successional species in logged forests, where 45% of the AGB accumulated was due to only two species (Astronium graveolens Jacq and Gallesia integrifolia (Spreng.) Harms). The opposite was observed in unlogged forest fragments, where two late successional hardwood species (Aspidosperma polyneuron Müll.Arg and Holocalyx balansae Micheli) accumulated 38% of the AGB. Our findings indicate that even decades after the last logging event semi-deciduous seasonal Atlantic Forest fragments with a selective logging history may present different AGB, structure, and functional composition from the expected pattern for old-growth forests in the given region.