Sustainable manufacturing has significant impact on a company’s business performance and competitiveness in today’s world. A growing number of manufacturing industries are initiating efforts to address sustainability issues; however, to achieve a higher level of sustainability, manufacturers need methodologies for formally describing, analyzing, evaluating, and optimizing sustainability performance metrics for manufacturing processes and systems. Currently, such methodologies are missing. This paper introduces a systematic decision-guidance methodology that uses the sustainable process analytics formalism (SPAF) developed at the National Institute of Standards and Technology. The methodology provides step-by-step guidance for users to perform sustainability performance analysis using SPAF, which supports data querying, what-if analysis, and decision optimization for sustainability metrics. Users use data from production, energy management, and a life cycle assessment reference database for modeling and analysis. As an example, a case study of investment planning for energy management systems has been performed to demonstrate the use of the methodology.