The expansive clay soils, which cover most of the new urbanized areas in Egypt, create major damages in most of the engineering structures and infrastructures such as buildings, roads, bridges, pipelines and others due to bad human activities, e.g. lack of maintenance for sewage and drinking lines, and flood irrigation of golf areas which causes fluctuation of water content through the foundation clay layers associated with shrink-swell behavior. These geotechnical challenges and their treatment solutions consume most of the urbanized project budget and delay the development plan. Therefore, in this study the high plasticity and soft to firm clay soils were stabilized using various dosages of fresh cement kiln dust (CKD) as an economical alternative to the other expensive stabilizing agents (stabilizers or binders) such as lime, cement and other chemical stabilizers. The effectiveness of this type of CKD as a stabilizing agent, soil stabilization mechanism, and changes in mineralogical and microstructural characteristics of stabilized soils due to this stabilization process were evaluated through Atterberg limits, unconfined compressive strength (UCS), stiffness (stress–strain behavior, Es), pH, electrical conductivity (EC), total dissolved solids (TDS), X-Ray diffraction (XRD) and scanning electron microscope (SEM) investigations. The present study revealed that by adding CKD, the workability of the treated clays was increased by decreasing the liquid limit and plasticity index as well as increasing the bearing capacity and decreasing the settlement by increasing UCS and Es. This study also showed that by adding CKD, the initial pH, EC, and TDS of CKD-clay system increased, creating favorable conditions for dissolution of edges and surfaces of clay flakes. The active montmorillonite clay flakes adsorbed the soluble calcium cation and sulfate anion on their surfaces that are rich in soluble silica and alumina and then the cation exchange and flocculation–agglomeration processes began. With curing, the pozzolanic products grew on the surfaces and edges of clay flakes and extended into the voids of the agglomerated inter-clay particles resulting in the filling of these micro-voids. The present investigation also found that, the progressive decreasing in pH, EC, and TDS values of CKD-clay systems through different curing periods is a good indicator for pozzolanic activity.