[6] On 25 June 2024, Berset was elected Secretary General of the Council of Europe, and assumed his role on 18 September 2024 succeeding Marija Pejčinović Burić.

During the COVID-19 pandemic in Switzerland, as head of the Federal Department of Home Affairs, he was one of the leading figures in the government's response to the crisis.

Following an interview with Berset, Schweizer Radio und Fernsehen (SRF) wrote, "there were moments during the first wave when he no longer knew whether it was day or night, weekday or weekend.

[18] In January 2024, Berset became the Swiss government's candidate to succeed Marija Pejčinović Burić as Secretary General of the Council of Europe, competing with Didier Reynders and Indrek Saar.

[19][20] On 21 November 2020, the weekly Die Weltwoche revealed, from the pen of the former Zürich SVP/UDC national councillor Christoph Mörgeli, that Berset was the victim of an attempted blackmail the previous year.

A woman, since convicted in criminal proceedings, allegedly tried to extort 100,000 Swiss francs from him by threatening to publish photographs and private messages that they had exchanged.

[21] The political world seized the case;[22] the Supervisory Authority of the Public Ministry of the Confederation (MPC) opened an investigation to verify that the Federal Councillor did not benefit from favours in the treatment of his complaint.

[23] In September 2021, while the health policy followed by the Federal Council to overcome the COVID-19 pandemic was contested and Alain Berset criticized, the case bounced back: a controversy broke out over the use of a vehicle of representation during an escapade with the woman, on the use of state collaborators to settle the attempt of blackmail, in particular by sending the Task Force TIGRIS of the Federal Judicial Police at the home of the person concerned, as well as on the limits between respect for the private life invoked by the magistrate and the public interest.