Abstract The paper deals with the development and presentation of the use of an advanced computational optimization tool for the conceptual planning of facilities in the field of waste-to-energy. The determination of the suitable capacity and sizing of an appropriate heat recovery system, according to adopted heat utilization strategy (i.e. either only electricity production or combined heat and power if feasible), represent crucial decisions about each individual incineration plant in its early project stage. The economic feasibility of the project should be guaranteed at the same time. The feasibility is measured by internal rate of return. An optimization model supporting such decisions was built and is introduced. Building a new incinerator, from the initial considerations to its full operation, is a long-term process with duration at a minimum of 5–7 years. The erection is then followed by an operational phase exceeding 20 years. The unclear future development of important parameters affecting the project sustainability is reflected by implementing principal concepts of stochastic programming. In the article, a brief overview of principal ideas related to decision making under uncertainty (wait-and-see and/or here-and-now approaches, specification, and use of scenarios) is given first, followed by the description of a mathematical model. Then, the selected approach is demonstrated through a case study involving a municipal solid waste incinerator.