This paper estimates the foodmiles (embedded distances) and transport-related carbon emissions of 27 Food Quality Scheme (FQS) products – Protected Designation of Origin (PDO), Protected Geographical Indications (PGI) and organic – and their reference products. It goes further than the existing literature by adopting a value chain perspective, instead of the traditional consumer perspective, and focusing on FQS products. The same methodology is applied across all the case studies. The article specifically investigates the determinants of differences between FQS and their references. FQS products travel significantly shorter distances (−30%) and generate significantly lower transport-related emissions (−23%) than conventional food products. The differences are even greater for vegetal and organic products. The relationship between distance and transport-related emissions is not exactly proportional and highlights the importance of transport modes and logistics, in particular for exports and imports. Finally, we stress the importance of the spatial distribution of the different stages in the value chains (e.g. production, processing). PDO technical specifications delimit a geographical area for production and processing, thereby limiting distances and transport-related emissions compared to conventional food products, but also compared to other types of FQS. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 678024.