Environmental efficiency should not be treated independently of production efficiency. Several studies have demonstrated that lean management can be a major part of the answer to improving the environmental performance of companies. In this context, this work integrates existing methodologies and approaches from lean thinking, Industry 4.0 and mathematical optimization and then presents a toolkit for integrating, measuring, controlling and improving production and environmental performance in companies. The proposed approach is the result of previous investigations and is being validated in companies in the agri-food sector.