Consideration for the energy consumption and environmental impacts is required depending on the changed capacity under a flexible and reconfigurable manufacturing environment. This article focuses on a holistic production planning approach in a reconfigurable manufacturing system. The energy consumption and material flows that are incurred on the reconfigurable manufacturing system are defined from the perspective of the processing plan describing how to make a part. The suggested energy estimation model integrates the existing literature and set up a newly modified model including diverse part handling systems such as automated guided vehicle and conveyor in more detail. Alternative system reconfigurations are analysed in order to dynamically evaluate the performance in terms of different holistic criteria such as the energy consumption, environmental effects and throughput. A production planning model with the multi-objective function for minimising the energy consumption and maximising the throughput is developed. The benefit coming from the adoption of suggested model has been addressed with reference to a real industrial use case study.