On 17 December 2013, Schwarzelühr-Sutter was appointed Parliamentary State Secretary at the Federal Ministry for the Environment, Nature Conservation, Building and Nuclear Safety in Merkel's third cabinet.

[11][12] In this capacity, she has represented successive ministers Barbara Hendricks (2013–2018) and Svenja Schulze (since 2018) in political and parliamentary affairs, particularly in her designated special areas of climate change mitigation, nuclear reactor safety, conservation, and the environment and health.

In the negotiations to form a coalition government under Merkel’s leadership following the 2017 federal elections, Schwarzelühr-Sutter was part of the working group on energy, climate protection and the environment, led by Hendricks, Armin Laschet and Georg Nüßlein.

Following the 2021 state elections in Baden-Württemberg, Schwarzelühr-Sutter was part of her party's delegation in negotiations with Minister-President Winfried Kretschmann's Alliance '90/Greens on a potential coalition government.

[26] In January 2016, in response to an incident at the Leibstadt Nuclear Power Plant in Switzerland, near the German border, and near her parliamentary constituency, Schwarzelühr-Sutter criticized the operator's attitudes to safety.