Food security and biodiversity conservation are closely interconnected challenges to be addressed to achieve a sustainable food system on a global scale. Due to the complex nature of food production and consumption system, quantifying the impacts of food supply chains on biodiversity is challenging. Life cycle assessment (LCA) allows for systematically addressing environmental impacts along supply chains, representing a reference methodology that can be applied for assessing food systems. In the present study, 32 representative food products of consumption in the European Union (EU) were selected and their environmental impacts calculated through a process-based LCA. The potential contribution of EU food consumption to the current biodiversity decline has been evaluated adopting both midpoint and endpoint indicators. A comparison of the impact drivers was performed. Meat products, the underpinning land use for agricultural purposes, and climate change represent the main hotspots of impacts on biodiversity. Notwithstanding several drivers of biodiversity loss can be accounted for with LCA, the evidence of the increasing biodiversity decline on both a European and a global scale indicates that the assessment system should be further expanded, especially for what concerns refining impact categories such as ecotoxicity, and including resource overexploitation, and impact due to invasive species. This study illustrates: how far the current LCA based impact assessment framework may help to address the drivers of biodiversity loss; which are the main uncertainties associated to results stemming from the application of different endpoint methods; which aspects need to be elaborated further to ensure a comprehensive assessment of biodiversity impacts due to food production and consumption.