The impact of tillage and puddling operations on the stability and physico-chemical properties of clay-humus complexes was investigated. The naturally occurring clay-humus complexes were isolated from surface and sub-surface layers of long-term experiment on tillage and puddling in a rice-wheat cropping system. The cation exchange capacity, stability against thermal activation (at 35 and 55°C) and microbial inoculation, were evaluated. The cation exchange capacity, of clay-humus complexes from no-tillage treatment was significantly higher than that from conventional tillage treatment. No-tillage increased stability of adsorbed labile humus against both thermal activation and microbial inoculation whereas no-puddling significantly increased stability only against microbial inoculation. There was significant interaction effect between tillage treatment and depth of sampling on thermal stability; such as thermal stability of clay-humus complexes from no-tillage at 0–15 cm depth and tillage (T) at 15–30 cm depth was at par, and significantly higher than that of no-tillage at 15–30 cm depth and T at 0–15 cm depth. In case of microbial decomposition, no significant interaction was found between tillage treatments and depth of sampling but there were significant interaction effect between tillage and microbial inoculation and between depth of sampling and microbial inoculation.