Sustainable development requires measures to decrease energy consumption and to avoid any harmful impact on the environment. In recent years, a lot of research has been focused on designing energy systems by emulating the natural ones. This can be regarded as a novel way to support the transformation to sustainable energy systems. The initial step in forming energy systems of thus type, by emulating the ecosystem approach, is the development of a model for rendering the current situation. To contribute to the solution of this problem, an ecosystem model combining the analysis, optimisation and simulation modules has been developed as part of this study. The commonly used models for energy systems are good predictors of the general energy dynamics and structures; however, they can be inadequate when it comes to describing or predicting the complex phenomena within energy systems, such as the large number of parameters, the many end-users, the potential of the technologies, the assessment of the various environmental impacts and the variety of resources. With the implementation of the ecosystem model there is further expanding of the knowledge of an advanced, self-organising methodology integrated within the model’s operation by emulating the natural system dynamics. The ecosystem model could become a valuable tool for developing sustainable energy systems, and allowing the development of the most suitable and sustainable energy system based on the local availability of energy sources.