Landscape transformation and atmospheric nutrient depositions, important global change drivers, are affecting the vegetation and soil properties of natural dry tropical forest and derived savanna ecosystems in India. This study assessed the effect of continuous N and P additions for 6 years on the size distribution and properties of soil aggregates in forest–ecotone–savanna gradient. Addition of N significantly increased the proportion of macroaggregates in forest and ecotone, whereas the same input significantly decreased their proportion in the savanna. Consequently, the stability of soil aggregates increased significantly in forest and ecotone, whereas it decreased significantly in the savanna. The effect of P addition on soil aggregate stability was marginal. N addition also altered the biological and chemical qualities of soil aggregates. It caused increase in microbial biomass C (MBC) associated with macroaggregates in forest and ecotone; however, in savanna, MBC increased in the microaggregates. P addition did not affect the amount of MBC in both types of soil aggregates. Because of rapid accumulation of applied N and P in the microbial biomass, the ratios of MBC to microbial biomass nitrogen (MBN) as well as microbial biomass phosphorous (MBP) were decreased in both aggregates. Overall, the effect of N addition was more marked than that of P addition, suggesting that N is more limiting than P in these dry tropical ecosystems. In the current scenario of N loading, continued soil N loading in forest may lead to increased macroaggregates with associated MBC and MBN and greater aggregate stability. In contrast, the extensively distributed savannas may show the reverse trend leading to a decrease in soil fertility.