The removal of chlorpyrifos (CLP) from the environment is a matter of general interest, because it is one of the most widely used insecticides in the world but presents a high toxicity and persistence in the environment. Biological strategies are considered as a good option to remediate different environmental compartments. Assisted natural attenuation was used to find the ability of different kinds of soils to mineralise CLP. In this way, two soils showed the capacity to degrade CLP (R and LL up to 47.3% and 61.4% after 100 d, respectively). Thus, two CLP-degrading strains, Bacillus megaterium CCLP1 and Bacillus safensis CCLP2 were isolated from them, showing the capacity to degrade up to 99.1 and 98.9% of CLP in a solution with an initial concentration of 10 mg L−1 after 60 d. Different strategies were considered for increasing the effectiveness of soil bioremediation: (i) biostimulation, using a nutrients solution (NS); (ii) bioaugmentation, using B. megaterium CCLP1 or B. safensis CCLP2; (iii) bioavailability enhancement, using randomly methylated β-cyclodextrin (RAMEB), a biodegradable compound. When bioaugmentation and RAMEB were jointly inoculated and applied, the best biodegradation results were achieved (around 70%). At the end of the biodegradation assay, a toxicity test was used to check the final state of the bioremediated soil, observing that when the degrading strains studied were individually inoculated into the soil, the toxicity was reduced to undetectable levels.