The Swedish risk management case of Baltic fatty fishes, in which dioxin levels may be too high, is a typical multidimensional food safety decision problem involving public health, economic, environmental and socio-cultural aspects. To effectively address the dioxin food safety problem, the multiple dimensions and conflicting interests of stakeholders have to be considered systematically when evaluating competing risk management options. The objectives of this study were to illustrate the applicability of the Multi-Criteria Decision Analysis (MCDA) method for multidimensional food safety risk management problems, and to evaluate the Swedish dioxin risk management using MCDA. The results show that the MCDA method is indeed a relevant tool for modelling the multifactorial Swedish dioxin problem and for initiating discussions amongst stakeholders to increase the acceptance of chosen strategies. Abolishing the derogation from the European Commission’s maximum limits for the presence of dioxins in Swedish fish is the dominant strategy for risk assessors, whereas the preferences provided by the other stakeholders would suggest a continuation of the derogation without providing consumer information. However, the preferences of female consumers match with the 2011 decision of the Swedish government to ask for a derogation in combination with consumer information. The conclusion drawn from our MCDA analysis is comparable to the government’s decision that—given the gradual reduction in dioxin concentrations in Baltic fish—the decision to continue providing consumer information or not mainly depends on how risk managers balance the preferences of the different stakeholders.