Industry 4.0 tools, such as the Internet of Things, artificial intelligence, digital twinning, and cloud computing, create a technological revolution that accelerates efforts to optimize the efficiency of cyber-physical operations and services. The waste management system requires a critical share of city logistics optimization, especially when using cyber-physical systems. Modern tools reduce the required municipal waste handling, such as loading and unloading, transportation, and warehousing, which leads to an increase in efficiency and flexibility, saving energy and time, and protecting the environment. In this paper, we present a cyber-physical waste management system solution by providing a cyber-physical model design and description, mathematical modeling, and two cases to investigate the impact on energy consumption and emissions. After an introduction and literature review, we describe the design of the cyber-physical model and tackle the first echelon. The designed system incorporates the IoT, smart bins with multi-percentage sensors, data and information analysis, vehicles’ actual routes, energy and emissions optimization, multi-echelon systems, time windows, and flexibility. Mathematical modeling equations for the optimized total energy consumption are presented. Thirty and twenty smart bins located in VIII District in Budapest are detailed as two case studies, where solutions for the optimized real routes and energy consumption are found using three metaheuristic algorithms: genetic, particle swarm, and simulated annealing optimization algorithms. The accrued emissions of CO, NMHC, CH4, NOx, and PM for the optimized solutions are calculated. Finally, the results are compared with a random traditional solution to measure the effectiveness.