In the upcoming years, the member countries of the European Union (EU) are expected to reach certain milestones with regards to different waste management policies: reducing the amount of generated waste, maximizing recycling and the energy usage of the appropriate waste types, phasing out landfilling, etc. With the increasing demands on these criteria comes also the need for the planning of the construction and modernization of the required waste processing infrastructure. This paper summarizes the current state of affairs for selected member countries of the EU and describes the possible technologies that are suitable for reaching the specific milestones. A multi-stage multi-period stochastic mixed-integer programming model is developed, with the goal to minimize the overall costs associated with reaching the milestones. This model describes well the sequential nature of the decision-making process. The present-day decisions must regard the possible effects of the decisions on the future. The planning considers the possible modernization of infrastructure which gradually increases the efficiency in order to hit the time-respective milestones. The model is presented on a case study which examines the situation in the Czech Republic divided into 13 regions, considering 27 scenarios for future development.