In recent years, waste management systems have been evaluated using a life cycle assessment (LCA) approach. A main shortcoming of prior studies was the focus on a mixture of waste with different characteristics. The estimation of emissions and consumptions associated with each waste fraction in these studies presented allocation problems. Waste-to-energy (WTE) incineration is a clear example in which municipal solid waste (MSW), comprising many types of materials, is processed to produce several outputs. This paper investigates an approach to better understand incineration processes in Spain and Portugal by applying a multi-input/output allocation model. The application of this model enabled predictions of WTE inputs and outputs, including the consumption of ancillary materials and combustibles, air emissions, solid wastes, and the energy produced during the combustion of each waste fraction.