Sustainability of an agricultural system is influenced by the management practices through their effect on soil properties and processes, and crop yields. Carbon Management Index (CMI) takes into account changes in total as well as labile carbon pools and thus is an important indicator of sustainability of cropping systems. Soil structure is closely linked with soil carbon pool, and serves another index of soil quality and sustainability. We investigated CMI and soil aggregation (water stable aggregates and aggregate porosity) in medium-textured soils (silt loam and silty clay loams) under different cropping systems (maize-wheat, rice-wheat, soybean-wheat, guinea grass and setaria grass) for the last 6 to 32 years, using organic and inorganic fertilizers, for assessing their sustainability. The total carbon (CT), labile carbon (CL), CMI, Mean Weight Diameter (MWD) and aggregate porosity varied significantly under different cropping systems. The range was 1.59 (R-W) - 4.29 % (Setaria) for CT, 1.23 (R-W) – 3.89 mg/kg (Guinea grass) for CL, 52.09 (R-W) – 129.77 (Guinea grass) for CMI, 0.90 (R-W) – 5.09 mm (Guinea grass) for MWD and 41.5 (R-W) – 56.8% (S-W) for aggregate porosity. Aggregate porosity was highest (56.8%) under S-W, followed by grasses (50.1-51.2%) and M/R-W (41.5-49.6%). The effect of fertilization on CMI and aggregation was studied in M-W and R-W systems. Balanced use of chemical fertilizers (NPK) gave the highest CMI, MWD and aggregate porosity, followed by absolute control; applications of N alone exhibited lowest values for these parameters. Integrated use of farm yard manure and chemical fertilizers further improved these values and the differences were statistically significant. Based on CMI and MWD values, sustainability of different cropping systems varied as: perennial grasses > soybean-wheat > maize-wheat > rice-wheat. Considering 100 CMI as a border line between sustainable and unsustainable system (CMI computed by considering undisturbed areas near the experimental plots as the reference), only perennial grasses were sustainable. However, if absolute control plots were considered as reference, CMI in N alone treatment was below 100, while in all other treatments it was >100. Considering 100% NPK as the reference plots, all treatments showed CMI <100, except 100% NPK + Lime, which gave a value of 107.72. According to these data, (a) 100% NPK sustained soil productivity, (b) addition of organics further improved sustainability of the system, (c) continued use of only N or NP fertilizers deteriorated soil productivity, and (d) maize-wheat and rice-wheat cropping showed almost similar effects on soil.