Combining mathematical programming and thermodynamic analysis for solving energy integration of industrial processes appears to be a very powerful tool to target minimum energy cost requirements. Defining the role played by thermodynamic analysis and numerical methods allowed us to define a generic method for calculating the energy integration even of complex industrial sites. The method has been adapted to solve combined energy and environments synthesis of industrial processes. In the approach, different alternative process schemes are included in this superstructure, the optimal structure being extracted using MILP optimization that minimizes the cost of energy, including raw materials, fuels and electricity, rather than just thermal energy. This new modelling approach, that allowed us to target process modifications and improvements has been named EMO (effect modelling and optimization). In the paper, we discuss how the approach has been extended to represent the environmental and energy interactions both in terms of objective functions and constraints. Having developed the mathematical tool, we discuss the role that this tool plays in the engineering method developed to reach combined energy and environmental targets in industrial processes. The generic method has been validated on applications in two major industries: one from the pulp and paper industry and one from the brewing industry. The example of the Kraft pulp process is used to illustrate the application of the approach.