After he was not considered for the country's cabinet in 2009, he took over from November 2009 until his appointment as interior minister in October 2010, the Office of the Presidents of the SPD parliamentary group and became a member of the Presidium of the State Parliament.

In the local elections in 2008, he was again chosen as a city councilor in the Municipal Assembly of Forst (Lausitz) and as a deputy in the district council Spree-Neisse.

Following the resignation of Rainer Speer 23 September 2010, Woidke was appointed by Platzeck on 6 October 2010 as the new interior minister and sworn in before parliament.

On 16 December 2010 the Brandenburg State Parliament approved the draft law on the merger of these authorities into a new police headquarters with effect from 1 January 2011.

In 2014, he assumed the office of Coordinator of German‑Polish Intersocietal and Cross‑Border Cooperation, whose task is to foster mutual understanding and trust and to propose concrete political solutions to the German and Polish Governments.

In the negotiations to form a Grand Coalition of Chancellor Angela Merkel's Christian Democrats (CDU together with the Bavarian CSU) and the Social Democrats (SPD) following the 2013 federal elections, Woidke was part of the SPD delegation in the working group on energy policy, led by Peter Altmaier and Hannelore Kraft.

In similar negotiations after the 2017 federal elections, he was part of the working group on economic policy, led by Thomas Strobl, Alexander Dobrindt and Brigitte Zypries.

Alongside Manuela Schwesig, Woidke was instrumental in the Bundesrat's 2020 selection of Ines Härtel as the Federal Constitutional Court's first judge from East Germany.