The reconfigurable manufacturing system (RMS) appears to be eco-friendly while coping with rapidly changing market demands. However, there remains a lack of discussion or research regarding sustainability or environment-friendly functions within RMS. In this study, the reconfiguration planning problem is introduced to represent the core issues within the RMS. Reconfiguration occurs depending on new demands or conditions in the company by reconfiguring machines, such as removing, adding, or changing parts, giving considerable consideration to arrangement of machines, known as configurations in RMS. Therefore, reconfiguration process is always strongly connected to cost, energy consumption, and, more importantly, data management. The complexity of reconfiguration, product variation, and development processes requires tools that are capable of managing multi-disciplinary bill-of-material(BOM) or product data and providing a better collaboration support for data/information tracking while maintaining sustainability. This paper proposes a multi-disciplinary green bill-of-material (MDG-BOM)—an improved Green-BOM concept—with an additional multi-disciplinary feature to minimize emissions and hazardous materials during product development, as well as manage product information across multiple disciplines during the reconfiguration process. A smart spreadsheet for managing MDG-BOM was developed to allow multiple departments to integrate multiple sources of CAD design data and monitor/track changes throughout each step of the process.