Soil structure is an important key in the bioremediation process; for instance, clay soils tend to have high absorption of pollutants and low rates of bioremediation due to their high plasticity and oxygen restrictions. This work assesses seven different treatments for contaminated clay soil using lime, silica nanoparticles, and both components in combination. After a three-month treatment, the variation of the soil granulometry, pH, porosity, cation exchange capacity (CEC), humidity, organic matter, respirometry, and humic acids were measured in order to evaluate the improvements regarding soil structure. Furthermore, total petroleum hydrocarbon (TPH), polycyclic aromatic hydrocarbons (PAHs) and heavy metals were monitored before and after the treatments. The combined treatment using lime and nanosilica presented the best results, reducing the percentage of clays from 61% to 5% and showing a relationship between improved of soil structure and the reduction of pollutants, with a 35% removal for TPHs being the highest obtained with the seven treatments.