The underlying values and priorities that drive policy responses depend largely on the constructs that researchers and decision makers select to measure and the metrics used. Despite much recent attention being given to sustainable diets and food systems and to the importance of clearly measuring sustainability to meet targets, to achieve goals, and to appraise dietary and environmental policies, it is not commonly agreed how the different indicators of sustainable diets are assessed. The evidence base for assessment of these indicators are frequently weak, fragmented, and arbitrary. The aim of this paper was to compare a range of published methods and indicators for assessing sustainable diets and food systems in order to harmonise them. Keyword and reference searches were performed in PubMed, Scopus, CAB Abstracts, and Web of Knowledge. Fifty-two studies (21 proposed methods and 31 used methods) that combined environment, nutrition and health, and socioeconomic aspects of sustainable diets were reviewed. The majority (over 90%) of the studies focused on high-income countries. Twenty-eight studies assessed the environmental effects of different dietary practices, eight of the studies examined the nutrition and health indicators used for assessing sustainable food systems, and seven studies assessed the social and economic costs of diets. A classification of the elements was developed, and common elements are proposed for standardizing. These elements were categorized into nutrition and health indicators, environment indicators, and socioeconomic indicators. Standardized or harmonized indicators can be used for consistency and applicability purposes and to support, implement, and monitor relevant policies.