Abstract In the past, various attempts have been made to alter the microbial composition of the soil. Moreover, considerable effort has been devoted to develop mechanisms to control the soil (micro)biological processes. Currently, a number of novel and powerful strategies are proposed to optimise the microbiota in order to achieve soil clean-up. Nevertheless, in practice the most relevant approach is the so-called intrinsic remediation, which often corresponds with minimal intervention. It is important for the scientist, the regulator and the practitioner to carefully weigh the social consequences of treatment such as `Isolating–controlling–monitoring' versus an approach based on `Binding and immobilization of the pollutants'.