This study explores a systematic strategy to design appropriate bioremediation projects for marginalized regions that have the potential to contribute to sustainable development in that region. Ecological Engineering (EE) is of particular value for the development of appropriate bioremediation technology for such regions but a stricter planning tool than provided by EE itself, is also needed when the goal of the project goes beyond remediation targets. The Framework for Strategic Sustainable Development (FSSD) applies basic principles for sustainability and includes a stepwise strategic planning mechanism for their application. The inclusion of EE within the FSSD may steer soil bioremediation projects in rural areas in developing countries and sparsely populated regions in industrialized countries towards sustainability. The utility of the approach was tested on two cases of soil pollution in marginalized regions: the Chinandega region in Nicaragua (pesticide polluted agricultural soil) and a former filling station (diesel polluted residual area) in Gäddede, northern Sweden. The study demonstrates how the inclusion of the EE key concepts within the FSSD may increase the utility of EE for strategic sustainable development within the region. No difficulties in terms of conflicting suggestions were found in the proposed integrated approach; the two tools were found to contribute on different aspects to provide support to project management and decision making.