Land-use change (LUC) in the tropics, such as the exponential rate of conversion of natural habitats into intense monocultures focusing on cash-crop cultivation, is a major causal factor of global environmental change. To understand the effects of LUC on soil organic matter (SOM) stability and the dynamics of C and N within SOM fractions, we measured the C and N content and delta C-13 and delta N-15 in fractions of different aggregate- and density-size of acric ferralsols in tropical rainforests and rubber plantations. The proportion of macroaggregates, heavy and light fractions significantly decreased after LUC. The results showed that, in general, conversion of tropical rainforest to rubber plantation significantly decreased the C and N content in bulk soil and the aggregate- and density-size to 20 cm soil depth. The decrease in C and N content in bulk soil was mainly driven by decreasing C and N associated with macroaggregates and light fractions, which accounted for > 50%. We found significant correlations among mean weight diameter, aggregate-, and density-size fractions C, N, and C/N ratios. The conversion of tropical rainforest to rubber plantation significantly enriched soil delta C-13 while depleting delta N-15. Enrichment of delta C-13 in rubber plantations could be explained by the mixing of old and fresh C. We conclude that, C and N dynamics within SOM fractions were greatly affected by LUC and the delta C-13 and delta N-15 signature confirms the changes in SOM stability after forest conversion. We suggest that planting intercrops within rubber monocultures may improve SOM accumulation, soil aggregation, and C and N sequestration.