Land-use changes with natural vegetation removal may impact the quantity and quality of humic substances (HS), including their molecular nature. Nuclear magnetic resonance (NMR) experiments were used in the present study to evaluate the alterations in the molecular composition of fulvic (FA) and humic (HA) acids from soils under eucalypt plantations in three major biomes in Brazil: Atlantic Forest, Cerrado, and Grassland. The major NMR-identifiable components in these HS were aromatics including aromatic C-O, COO/NC = O groups, peptides, carbohydrates, lignin-derived moieties and nonpolar alkyls. In all biomes the dipolar dephasing technique indicated the presence of significant amounts of condensed aromatic C, possibly inherited from charred materials derived from natural and anthropogenic fires in the region. The nonpolar alkyl C to O-alkyl C ratio averaged 1.4 for HA and 1.1 for FA. Humic substances from eucalypt soils showed greater contribution of nonpolar alkyl groups and a smaller abundance of O-alkyl groups in comparison to the native vegetation soil. Sugarcane (Saccharum officinarum L.) cultivation increased HA aromatics in comparison to those from the native Atlantic Forest soil, but when sugarcane was substituted by eucalypt the aromatics decreased and O-alkyl C recovered in HA and FA. There was evidence of greater contribution of lignin-derived C for HA and FA in sites planted with Brachiaria spp. pastures. Except for the HA from one Cerrado soil (Itacambira), aromaticity of HA decreased following planting to eucalypt. These changes in HS molecular composition across biomes may have impact on soil organic matter processes and they should be taken into account in future studies.