Assessing the overall effects of organic food systems is important, but also a challenge because organic food systems cannot be fully assessed from one single research perspective. The aim of our research was to determine the role of values in assessments of organic food systems as a basis for discussing the implications of combining multiple perspectives in overall sustainability assessments of the food system. We explored how values were embedded in five research perspectives: (1) food science, (2) discourse analysis, (3) phenomenology, (4) neoclassical welfare economics, and (5) actor-network theory. Value has various meanings according to different scientific perspectives. A strategy for including and balancing different forms of knowledge in overall assessments of the effects of food systems is needed. Based on the analysis, we recommend four courses of action: (1) elucidate values as a necessary foundation for research assessment across perspectives; (2) openly discuss the choice of perspective, because it is decisive; (3) formulate common goals that can be translated into the different perspectives; and (4) consider assessment of food system sustainability a learning process and design it as such.