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This article considers the problem of the evaluation of the sustainability of heterogeneous process systems, which can have different areas of focus: from single process operations to complete supply chains. The proposed method defines exergy-based concepts to evaluate the assets, liabilities, and the exergy footprint of the analysed process systems, ensuring that they are suitable for Life Cycle Assessment. The proposed concepts, evaluation framework and cumulative Exergy Composite Curves allow the quantitative assessment of process systems, including alternative solutions. The provided case studies clearly illustrate the applicability of the method and the close quantitative relationship between the exergy profit and the potential sustainability contribution of the proposed solutions. The first case study demonstrates how the method is applied to the separation and reuse of an acetic-acid-containing waste stream. It is shown that the current process is not sustainable and needs substantial external exergy input and deeper analysis. The second case study concerns Municipal Solid Waste treatment and shows the potential value and sustainability benefit that can be achieved by the extraction of useful chemicals and waste-to-energy conversion. The proposed exergy footprint accounting framework clearly demonstrates the potential to be applied to sustainability assessment and process improvement while simultaneously tracking different kinds of resources and impacts.