Life cycle Assessment (LCA) is increasingly being applied as a decision variable in supply chain design and planning models. However, the lack of standardized guidelines in its application, raises questions regarding the usefulness and validity of the results obtained in these studies. This study aims to assess the impact of different approaches in the Life Cycle Inventory (LCI) and Life Cycle Impact Assessment (LCIA) steps of LCA on supply chain design and planning decisions. A multi-objective optimization-based methodology is applied to a case-study in the pulp and paper industry. Environmental and economic objectives are considered. Results show that different LCIA methods as well as different normalization data sets result in significant changes in the pool of possible solutions. However, different system models at the LCI step, different cultural perspectives and variations in the characterization factors tend to lead to the same strategic decisions. Important insights are gained regarding the impact of non-standardized analysis of the application of LCA in supply chain design and planning models. Furthermore, the importance of optimization models to improve LCA-based studies is highlighted in this work.