The key obstacle to environmental management information systems (EMIS) is how to efficiently integrate them into enterprise application environments. While there is considerable work on technical aspects of the problem, there are few suggestions of how to solve the problem on the conceptual level, in particular with dynamic business environments, mass customization and flexible manufacturing systems in mind. In this contribution, the Petri net theory is applied as an innovative conceptualization for providing transformation capabilities between widely-used enterprise resource planning (ERP) systems and material flow oriented EMIS.