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, Flachsbarth was part of the CDU/CSU delegation in the working group on energy policy, led by Peter Altmaier and Hannelore Kraft. From 2014 to 2018, Flachsbarth served as Parliamentary State Secretary at the Federal Ministry of Food and Agriculture, under the leadership of minister Christian Schmidt, in Merkel's third cabinet. During that time, she unsuccessfully ran for the office of president of the Central Committee of German Catholics (ZdK) in 2015; the post instead went to Thomas Sternberg.