For flexible manufacturing systems, there are normally some durations in which a number of machines are idle and do not process any parts. Devising a control policy to turn off the idle machines and reduce their level of energy consumption is a significant contribution towards the green manufacturing paradigm. This paper addresses the design of such a control strategy for a closed-loop flow shop plant based on a one-loop pallet system. The main goal is to coordinate running of the machines and motion of pallets to gain the minimal energy consumption in idle machines, as well as to obtain the desired throughput for the plant. To fulfill this goal, first mathematical conditions, which economically characterize the on-off control for machines, are presented. Constrained to these conditions and the mathematical models describing the pallet system, a mixed integer nonlinear minimization problem with the energy monitor as the objective function is then developed. Provided that the problem computation time can be managed, the optimal control for the operation of the plant and the minimal energy consumption in the idle machines are computed. To deal with the time complexity, a linearized form of the model and a heuristic approach are introduced. These methods are applied to some examples of industrial size, and their impacts in practice are discussed and verified by using a discrete event simulation tool.