Maintaining soil physical properties and organic C is the goal for sustainable use of soil resources in agroecosystems. The objectives of this research were to evaluate the changes in soil structure and C pools and to quantify the availability of labile C pools. The study site was in Bengkulu Province Sumatra, Indonesia. Four common agroecosystems were used to determine soil physical properties including bulk density, porosity, and soil aggregates. Labile soil C pools examined were particulate organic C (POC), microbial biomass C (MBC) and C mineralization (C min). Farming practices significantly affected the bulk density, macro-porosity, micro-porosity, aggregate stability(AS), mean weight diameter (MWD) and aggregation ratio (AR). However, the responses from treatments depend upon the soil depth. In general, agroforestry and fallow fields provided lower bulk density, higher porosity, AS, MWD and AR compared to rubber tree plantation and grain cropping. As a general trend, the values of POC, MBC and C min decreased in the order of agroforestry > fallow field > rubber tree plantation > grain cropping. The order of labile C pools in all fields were POC > MBC > C min. Significant increases (32 – 62%, p<0.05) in the soil organic C content was observed in agroforestry and fallow fields compared to rubber tree plantation and grain cropping systems at the depth of 0 – 20 cm. The highest available POC (43 to 82%) and MBC (2 to 5%) were found in agroforestry and fallow field. Mineralized C was about 2% in all fields indicating similar amount of active C from soil organic matter. In conclusion, improvement in soil structure properties, TOC, POC and MBC in agroforestry andfallow fields indicates better soil C sequestration and soil quality in these agroecosystems.Keywords: Aggregation, carbon mineralization, microbial biomass carbon, particulate organic carbon, rubber plantation[How to Cite: Handayani IP and P Prawito. 2013. 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