The integration of increasing shares of intermittent renewable energy necessitates flexibility in both energy generation and consumption. Typically, the operation of flexible energy resources is orchestrated through optimization models. However, the manual creation of these models is a complex and error-prone task, often requiring the expertise of domain specialists. This work introduces a methodology for the automatic generation of optimization models for systems of flexible energy resources to simplify the modeling process and increase the use of energy flexibility. This methodology utilizes a modular, generic model structure designed to depict systems of flexible energy resources. It incorporates algorithms for model parameter derivation from operational data and an information model that represents the system’s structure and dependencies of resources. The efficacy of this methodology is demonstrated in two case studies, highlighting its relevance and ability to significantly streamline the optimization modeling process by minimizing the need for manual intervention.