This study analyzes the environmental efficiency of the agricultural sector regarding the use of mineral fertilizers in the period 2001–2012 for a group of European countries. Specifically, efficiency is assessed through a dynamic Data Envelopment Analysis methodology. This method aims to analyze temporal efficiency changes through the estimation of Malmquist indexes with increasing and decreasing temporal windows. Findings show that most countries register efficiency advances in the periods 2002–2003 and 2007–2008. Specific countries, such as Belgium-Luxembourg, Denmark, Netherlands, Sweden and United Kingdom, register persistently higher values of the estimated Malmquist indexes. This study contributes to the existing literature by assessing country-specific efficiency paths, as well as by identifying best-performing countries from which lessons can be learnt. A brief review of main measures taken by a selected group of benchmark countries is offered. •Environmental efficiency patterns in managing fertilizer use are analyzed for a group of EU states between 2001 and 2012.•Inter-period changes in efficiency patterns are assessed through Malmquist indexes.•Most countries made significant advances in reducing fertilizer-use intensity in the periods 2001–2003 and 2006–2007.•Benchmark countries are identified based on increasing and decreasing temporal-windows approaches.•Main management initiatives and policies in selected benchmark countries are described.