Background: Two carbon (C) sources are of particular interest for soil organic carbon (SOC) storage under nitrogen (N) deposition: 1) glomalin-related soil protein (GRSP) and 2) microbial residual carbon (MRC) derived from microbial metabolites and residues. Both soil C sources are purported to have long residence times, but their contribution to SOC may be modified by changing soil N status. Methods: We assessed how N deposition influences GRSP and MRC as sources of SOC using soils from a long-term (11 years) N-addition site in a tropical forest in south China. We assessed differences in MRC and GRSP, microbial biomarkers, soil physico-chemical properties, and particle-size fractions between N-fertilized soils and controls. Results: Total GRSP, MRC, and SOC concentrations were higher under N-addition, but soil microbial biomass and community composition were largely unaffected, indicating that higher GRSP and MRC concentrations resulted from long-term accumulation and reduced microbial degradation. However, the relative contributions of GRSP or MRC to SOC were unchanged or lower than the controls due to a greater contribution of other C sources to SOC which were largely unstabilized by association with soil minerals. Conclusion: Tropical forests have great potential for SOC sequestration in response to N deposition which may help mitigate climate change. However, most of the additional SOC in N-fertilized soils was not associated with soil minerals, and thus prone to decomposition.