Groote served as a Member of the European Parliament from 2005, when he took over the seat vacated by Garrelt Duin. He has since been a member of the Committee on the Environment, Public Health and Food Safety. In this capacity, he participated in the 2007 United Nations Climate Change Conference in held in Bali; the 2008 United Nations Climate Change Conference in Poznań; the 2013 United Nations Climate Change Conference in Warsaw; and the 2015 United Nations Climate Change Conference in Paris. He also was his political group's shadow rapporteur for a 2008 report on including aviation within the European Union Emission Trading Scheme. In 2012, he replaced fellow Social Democrat Jo Leinen as chair of the committee, a position he held until 2014. From 2014, he was the coordinator of the Group of Socialists and Democrats in committee as well as the parliament's contact person for the European Medicines Agency (EMA).