Following the 2006 Swedish elections which saw the victory of the centre-right coalition of Fredrik Reinfeldt, Malmström returned to Sweden to take up the job of Minister for European Affairs in Prime Minister Reinfeldt's cabinet, which took office on 6 October 2006. Her responsibilities included institutional issues, review of the EU budget, Baltic Sea Strategy, the Lisbon Strategy and coordinating the Swedish Presidency of the Council of the European Union in 2009.