For different reasons (like increasing energy prices) energy consumption is more and more an issue of strong interest in manufacturing companies nowadays. Besides considering single processes/machines, the perspective on process chains and factories as a whole bears further potentials for improvement. In this context, dynamic interactions of different processes as well as auxiliary equipments (e.g. compressed air generation) need to be taken into account when planning and controlling manufacturing systems. Against this background in this work an innovative and comprehensive methodology with a generic energy flow oriented manufacturing simulation environment as core element is developed and embedded into a step-by-step application cycle. The concept as a whole is applied to several very different case studies (aluminium die casting, weaving mill, printed circuit board assembly) in order to demonstrate the broad applicability and potentials.