Biowaste compost can influence soil organic matter accumulation directly or indirectly. A 5-year experiment was conducted to assess the influence of biowaste compost on the process of soil aggregation and soil organic carbon(SOC) accumulation in a Mediterranean vegetable cropping system. The study involved four treatments: biowaste compost(COM), mineral NPK fertilizers(MIN), biowaste compost with half-dose N fertilizer(COMN), and unfertilized control(CK). The SOC stocks were increased in COM, COMN, and MIN by 20.2, 14.9, and 2.4 Mg ha~(-1)over CK, respectively. The SOC concentration was significantly related to mean weight diameter of aggregates(MWD)(P < 0.05, R~2= 0.798 4) when CK was excluded from regression analysis. Compared to CK, COM and COMN increased the SOC amount in macroaggregates(> 250 μm) by 2.7 and 0.6 g kg~(-1)soil, respectively, while MIN showed a loss of 0.4g kg~(-1)soil. The SOC amount in free microaggregates(53–250 μm) increased by 0.9, 1.6, and 1.0 g kg~(-1)soil for COM, COMN, and MIN, respectively, while those in the free silt plus clay aggregates(< 53 μm) did not vary significantly. However, when separating SOC in particle-size fractions, we found that more stable organic carbon associated with mineral fraction < 53 μm(MOM-C) increased significantly by 3.4, 2.2, and 0.7 g kg~(-1)soil for COM, COMN, and MIN, respectively, over CK, while SOC amount in fine particulate organic matter(POM) fraction(53–250 μm) increased only by 0.3 g kg~(-1)soil for both COM and COMN, with no difference in coarse POM > 250 μm. Therefore, we consider that biowaste compost could be effective in improving soil structure and long-term C sequestration as more stable MOM-C. Biowaste compost can influence soil organic matter accumulation directly or indirectly. A 5-year experiment was conducted to assess the influence of biowaste compost on the process of soil aggregation and soil organic carbon (SOC) accumulation in a Mediterranean vegetable cropping system. four treatments: biowaste compost (COM), mineral NPK fertilizers (MIN), biowaste compost with half-dose N fertilizer (COMN), and unfertilized control (CK). The SOC stocks were increased in COM, COMN, and MIN by 20.2, 14.9, and 2.4 Mg ha ~ (-1) over CK, respectively. The SOC concentration was significantly related to mean weight diameter of aggregates (MWD) (P <0.05, R ~ 2 = 0.798 4) when CK was excluded from regression analysis . Compared with CK, COM and COMN increased the SOC amount in macroaggregates (> 250 μm) by 2.7 and 0.6 g kg -1 soil, respectively, while MIN showed a loss of 0.4g kg -1 soil. The SOC amount in free microaggregates (53-250 μm) increased by 0.9, 1.6, and 1.0 g kg -1 soil For, COMN, and MIN, respectively, while those in the free silt plus clay aggregates (<53 μm) did not vary significantly. However, when separating SOC in particle-size fractions, we found that more stable organic carbon associated with mineral fraction <53 μm (MOM-C) increased significantly by 3.4, 2.2, and 0.7 g kg -1 soil for COM, COMN, and MIN, respectively, over CK, while SOC amount in fine particulate organic matter fraction (53-250 μm) increased only by 0.3 g kg -1 soil for both COM and COMN with no difference in coarse POM> 250 μm. Therefore, we consider that biowaste compost could be effective in improving soil structure and long-term C sequestration as more stable MOM-C.