Context Agricultural intensification leads to land use changes with potential consequences for soil aggregate stability and size distribution, affecting nutrient and water retention capacity, aeration, sequestration of soil organic carbon, and biogeochemical cycling. Aims This study evaluated soil aggregate stability and size distribution under potato, fallow and Eucalyptus globulus L. land uses in Cambisols of the eastern branch of the Central Andes, Bolivia. We also investigated the relation between aggregates and total C, extractable C, oxy-hydroxides, microbial biomass and activity. Methods Aggregate stability, size distribution and oxy-hydroxides were measured in soil samples from eight plots of each land use. Key results Compared to fields cultivated with potato (Solanum tuberosum L.), Eucalyptus increased aggregate stability, megaaggregate content, and C and N in the free silt + clay fraction. Fallow did not lead to significant changes in soil structure. Soil aggregate stability was related to both microbial biomass and oxy-hydroxides. Microbial biomass C, microbial activity and dithionite extractable Fe were positively related to megaaggregates and aggregate stability. Oxalate extractable Fe and Mn were related to microaggregates. Conclusions The plantation of Eucalyptus is suitable for soil structural amelioration and C sequestration, but its introduction to cultivated areas should be carefully evaluated due to its effects on soil chemistry and microbiology. Short-term fallowing did not contribute to the maintenance of soil structure. Implications In a context of land uses change, modifications of microbial biomass and activity would affect megaaggregate formation and stability. Alternative management practices are required to maintain soil structure and optimize sustainable land use of cultivated and fallow fields.