In late 2013, incoming FDP chairman Christian Lindner nominated Beer for the office of Secretary General; on 7 December 2013 she got elected (with 84.3% of all votes.

In September 2018, Beer announced that she would lead the FDP list and run for a parliamentary seat in the 2019 European elections.

[10] In parliament, she served as a Vice-President; she was part of its leadership under Presidents David Sassoli (2019–2022) and Roberta Metsola (2022–2023).

[11] She also joined the Committee on Industry, Research and Energy, where she has served as rapporteur on the Critical Raw Materials Act.

[14] In 2023, Beer was nominated by the government of Chancellor Olaf Scholz to become one of the vice-presidents of the European Investment Bank (EIB).

[21] In contrast to Beer's statement, the greater magnitude and probability of "extreme weather events" has been deemed to be linked to human activity since the IPCC Sixth Assessment Report.

[22] Beer has been an outspoken proponent of Taiwan’s independence; in 2022, she made an official trip to Taipeh and met with President Tsai Ing-wen.