Stabilization of organic matter (OM) against decomposition and its de-stabilization leading to mineralization, are important processes in the control of greenhouse gas emissions and carbon sequestration in soils. Soil organisms, particularly earthworms, may influence these processes greatly through their potential impacts on the interaction of OM with clay minerals, which is a mechanism which may protect OM for medium (years) to long (decades, centuries) time scales. The aim of this study was to use earthworms and pure minerals in order to investigate enhancement of carbon sequestration through the formation of aggregates containing particulate OM and organo-mineral associations, during a composting experiment. To this end we compared OM transformations in composting treatments with and without (i) clay minerals (montmorillonite) and (ii) epigeic earthworms (Eisenia andrei and Eisenia foetida). We used density fractionation of the end-products to quantify the amount of aggregates, including organomineral associations, formed during 196 days. Chemical composition and stability were examined by elemental analyses, Rock-Eval 6 thermal analysis and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The results indicated that the addition of minerals led to the formation of heavy fractions, most probably containing aggregates and organo-mineral associations, in treatments with and without earthworms. While OM showed higher oxidative transformation in all treatments, addition of earthworms changed organic carbon (OC) and nitrogen (N) concentrations in specific density fractions and increased the thermal stability of OM in heavy density fractions. These fractions contained higher proportions of aromatic and proteinaceous materials. We conclude that, earthworms under composting conditions, earthworms may be able to effectively to stabilize OM through the formation of aggregates and/or organo-mineral associations containing greater proportions of microbially-derived material.