Designing a food supply chain for a completely new product involves many stakeholders and knowledge from disciplines in natural and social sciences. This paper describes how Multi Criteria Decision Making (MCDM) facilitated designing a food supply chain in a case of Novel Protein Foods. It made the procedure transparent and aided the evaluation of alternatives. Two models, namely the Multi Attribute Value Theory (MAVT) and the Analytic Hierarchy Process (AHP), were used, due to the ease with which they handle a mix of quantitative and qualitative information, quantify the qualitative information and generate an overall value for each alternative. The resulting preference order differed mainly due to the manner in which criteria weights were elicited, alternatives scored and the use of scales in MAVT versus the pairwise comparison in AHP. However, the preference order of the top criteria with both methods was the same and weights were similar.