Direct seeding on permanent soil cover (DSPSC) systems can produce a large amount of residues to improve crop yields and soil properties, such as soil organic carbon (SOC) storage and soil aggregation. A long-term (11 years) trial, located in Antsirabe (subtropical climate, 16°C, 1300 mm.y-1) on a clayey andic dystrustept, has been used in order to study SOC storage, soil aggregate stability and SOC physical protection against microbial mineralization. The treatments were: (i) control (CT): annual rotation of maize (Zea mays L.) and soybean (Glycine max) with conventional tillage (hand ploughing), (ii) the same rotation with no tillage (NTm), (iii) a maize/maize rotation with legume (Desmodium uncinatum) permanent cover crop, and no-tillage (NTd), (iv) and a common bean (Phaseolus vulgaris)/soybean rotation with kikuyu grass (Pennisetum clandestinum) permanent cover crop, and no-tillage (NTk). No residues were exported in DSPSC systems and they were removed for CT system. Soil C content was significantly greater in NTm, NTd and NTk than in CT for only the 0-5 cm layer. Storage of organic soil C (in equivalent soil mass of 0-20 cm layer) was significantly greater in NTd and NTm than in NTk and CT. The annual rate of soil C storage for NTm and NTd were respectively 0.69 and 1.01 Mg C.ha-1 year-1. Water-stable macroaggregates (200-2000 [mu]m) were significantly greater in NTm, NTk and NTd than in CT at 0-5 and 5-10 cm layers. Macroaggregates were significantly correlated with soil C content. However, the C physically protected from mineralization was only about 50 and 200 [mu]gC g-1 soil in CT and NTm respectively, and not significantly between these two systems. The results showed that the tested systems, through the increase of organic inputs and the decrease of C loss, can significantly increase SOC stocks and soil aggregate stability. The stored C was physically protected against microbial mineralization by its localization into macroaggregates but at a low level.