The European Parliament recently called for urgent measures to halve food waste in the EU, where consumers are responsible for a major part of total waste along the food supply chain. Due to a lack of data on national food waste statistics, uncertainty in (consumer) waste quantities (and the resulting associated quantities of natural resources) is very high, but has never been previously assessed in studies for the EU. Here we quantify: (1) EU consumer food waste, and (2) associated natural resources required for its production, in term of water and nitrogen, as well as estimating the uncertainty of these values. Total EU consumer food waste averages 123 (min 55–max 190) kg/capita annually (kg/cap/yr), i.e. 16% (min 7–max 24%) of all food reaching consumers. Almost 80%, i.e. 97 (min 45–max 153) kg/cap/yr is avoidable food waste, which is edible food not consumed. We have calculated the water and nitrogen (N) resources associated with avoidable food waste. The associated blue water footprint (WF) (the consumption of surface and groundwater resources) averages 27 litre per capita per day (min 13–max 40 l/cap/d), which slightly exceeds the total blue consumptive EU municipal water use. The associated green WF (consumptive rainwater use) is 294 (min 127–max 449) l/cap/d, equivalent to the total green consumptive water use for crop production in Spain. The nitrogen (N) contained in avoidable food waste averages 0.68 (min 0.29–max 1.08) kg/cap/yr. The food production N footprint (any remaining N used in the food production process) averages 2.74 (min 1.02–max 4.65) kg/cap/yr, equivalent to the use of mineral fertiliser by the UK and Germany combined. Among all the food product groups wasted, meat accounts for the highest amounts of water and N resources, followed by wasted cereals. The results of this study provide essential insights and information on sustainable consumption and resource efficiency for both EU policies and EU consumers.