Humic materials make important contributions to soil organic carbon (C) and nitrogen (N) accumulation. However, information on the correlation between humic substances and the accumulation of soil aggregate-protected C and N in response to biochar application under tropical agroecosystems is limited. Therefore, a field trial was conducted to elucidate the effects of biochar on soil aggregate properties and humic materials and how these humic compounds affect aggregate-protected C and N in a humid tropical agroecosystem. The treatments included no-biochar control (CK), 15 Mg biochar ha-1 (BC-15), 30 Mg biochar ha-1 (BC-30), and 30 Mg biochar ha-1+ phosphate fertilizer (BC-30+P). The treatments BC-30 and BC-30+P significantly increased the contents of humic materials (humic and fulvic acids) as compared to CK. There was a significant increase in the mean-weight diameter of soil aggregates by 3- and 4-fold in BC-30 and BC-30+P, respectively. Similarly, BC-30 and BC-30+P led to significant increases in soil structural coefficient by 3- and 4-fold, respectively, relative to CK. Significant increases in organic C and N accumulation were observed in the macroaggregates of the biochar-amended soils. Inverse relationships between the degree of polymerization and aggregate-protected C and N were observed, implying that low-molecular-weight aliphatic compounds favor organic C and N accumulation with biochar amendments. The important soil property that contributed to organic C and N accumulation in aggregates was fulvic acid content, which could be used as an early and sensitive indicator to notice early changes in aggregate-protected C and N accumulation in soils of the humid tropics.