This paper proposes a new index for a comprehensive and systematic measurement of sustainability and throughput performance in production systems. The proposed index, called Sustainable Overall Throughput Effectiveness (S.O.T.E.), is designed on the basis of a comparison of the environmental and operational factors. Specifically, it integrates the following four dimensions: availability, utilization, performance, and environmental sustainability. The way each dimension is measured is explained and justified. This index uses the overall environmental equipment effectiveness (OEEE) index, which is based on the Overall Equipment Effectiveness (OEE) index. However, such metrics are lacking at the factory level, because OEEE, as well as the OEE, is devoted to equipment-level. Its application and potential contribution to the analysis of sustainable throughput is demonstrated through a case study in an actual crushing plant. Through examining several hypotheses concerning the relationship between operational and environmental performance, a series of useful conclusions could be raised. The main difference and advantage of the proposed S.O.T.E. is that S.O.T.E., as it is based on the Overall Throughput Effectiveness (OTE), measures factory-level sustainability and operational performance. S.O.T.E. allows us to relate the impact of the overall effectiveness of each one of the components of the index to each piece of equipment that makes a part of the production systems. Furthermore, S.O.T.E., as OTE, take into account the production system configuration (series, parallel, assembly, etc.).