Sustainability assessments bring together different perspectives that pertain to sustainability in order to produce overall assessments and a wealth of approaches and tools have been developed in the past decades. But two major problematics remain. The problem of integration concerns the surplus of possibilities for integration; different tools produce different assessments. The problem of implementation concerns the barrier between assessment and transformation; assessments do not lead to the expected changes in practice. This paper aims to analyze issues of complementarity in sustainability assessment and transformation as a key to better handling the problems of integration and implementation. Based on a generalization of Niels Bohr’s complementarity from quantum mechanics, we have identified two forms of complementarity in sustainability assessment, observer stance complementarity and value complementarity. Unlike many other problems of sustainability assessment, complementarity is of a fundamental character connected to the very conditions for observation. Therefore complementarity cannot be overcome methodologically; only handled better or worse. Science is essential to the societal goal of sustainability, but these issues of complementarity impede the constructive role of science in the transition to more sustainable structures and practices in food systems. The agencies of sustainability assessment and transformation need to be acutely aware of the importance of different perspectives and values and the complementarities that may be connected to these differences. An improved understanding of complementarity can help to better recognize and handle issues of complementarity. These deliberations have relevance not only for sustainability assessment, but more generally for transdisciplinary research on wicked problems.