In the European Parliament, Kristensen sat on the European Parliament's Committee on Fisheries, the Committee on the Internal Market and Consumer Protection and the Delegation for Relations with the Countries of South-East Europe.

On 3 October 2011 Kristensen was appointed to the post of Minister for Transport in the Cabinet of Helle Thorning-Schmidt, and left office on 9 August 2013.

On 10 October 2014 he again entered the cabinet, when he was appointed the position of Minister for Employment.

On 21 June 2019 Kristensen was appointed speaker of the Danish parliament, replacing Pia Kjærsgaard.

In 2011 Denmark was to appoint a president of the Nordic Council and Kristensen was chosen.