In order to increase the exploitation of the renewable energy sources, the diffusion of the distributed generation systems is grown, leading to an increase in the complexity of the electrical, thermal, cooling, and fuel energy distribution networks. With the main purpose of improving the overall energy conversion efficiency and reducing the greenhouse gas emissions associated with fossil fuel based production systems, the design and the management of these complex energy grids play a key role. In this context, an in-house developed software, called COMBO, presented and validated in Part I of this study, has been applied to a case study in order to define the optimal scheduling of each generation system connected to a complex energy network. The software is based on a nonheuristic technique, which considers all the possible combination of solutions, elaborating the optimal scheduling for each energy system by minimizing an objective function based on the evaluation of the total energy production cost and energy systems' environmental impact. In particular, the software COMBO is applied to a case study represented by an existing small-scale complex energy network, with the main objective of optimizing the energy production mix and the complex energy networks yearly operation depending on the energy demand of the users. The electrical, thermal, and cooling needs of the users are satisfied with a centralized energy production, by means of internal combustion engines, natural gas boilers, heat pumps, compression, and absorption chillers. The optimal energy systems' operation evaluated by the software COMBO will be compared to a reference case, representative of the current energy systems setup, in order to highlight the environmental and economic benefits achievable with the proposed strategy.