The dataset Sustainability performance of certified and non-certified food (https://www.doi.org/10.15454/OP51SJ) contains 25 indicators of economic, environmental, and social performance, estimated for 27 certified food value chains and their 27 conventional reference products. The indicators are estimated at different levels of the value chain: farm level, processing level, and retail level. It also contains the raw data based on which the indicators are estimated, its source, and the completed spreadsheet calculators for the following indicators: carbon footprint and food miles. This article describes the common method and indicators used to collect data for the twenty-seven certified products and their conventional counterparts. It presents the assumptions and choices, the process of data collection, and the indicator estimation methods designed to assess the three sustainability dimensions within a reasonable time constraint. That is: three person-months for each food quality scheme and its non-certified reference product. Several prioritisations were set regarding data collection (indicator, variable, value chain level) together with a level of representativeness specific to each variable and product type (country and sector). Technical details on how relatively common variables (e.g., number of animals per hectare) are combined into indicators (e.g., carbon footprint) are provided in the full documentation of the dataset.