The management of the increasing volume of municipal solid waste is an essential activity for the health of the environment and of the population. The organic matter of waste deposited in landfills is subject to aerobic decomposition processes, bacterial aerobic decomposition, and chemical reactions that release large amounts of heat, biogas, and leachates at high temperatures. The control of these by-products enables their recovery, utilization, and treatment for energy use, avoiding emissions to the environment. UAVs with low-cost thermal sensors are a tool that enables the representation of temperature distributions for the thermal control of landfills. This study focuses on the development of a methodology for the generation of 3D thermal models through the projection of TIR image information onto a 3D model generated from RGB images and the identification of thermal anomalies by means of photointerpretation and GIS analysis. The novel methodological approach was implemented at the Meruelo landfill for validation. At the facility, a 4D model (X,Y,Z temperature) and a 13.8 cm/px GSD thermal orthoimage were generated with a thermal accuracy of 1.63 °C, which enabled the identification of at least five areas of high temperatures associated with possible biogas emissions, decomposing organic matter, or underground fires, which were verified by on-site measurements and photointerpretation of the RGB model, in order to take and assess specific corrective measures.