In early 2006, after he lost the presidency of the PDC to Soledad Alvear, Zaldívar became a vocal critic of the Chilean economic system and voiced his disappointment with the government's "unwillingness" to amend it. He frequently came into conflict with Alvear and in August 2007 the Christian Democrat Party's Supreme Tribunal chastised him for his criticisms. Additionally, he was one of the harshest critics of the Transantiago public transport system, created under the leadership of the Concertación coalition to which the Christian Democrats belonged. In November 2007, Zaldívar, together with senators from the Alliance for Chile and independents Fernando Flores and Carlos Bianchi, voted against continued funding for the Transantiago, against the wishes of his party's leadership. Alvear and her followers accused Zaldívar of "siding with the right" and requested his expulsion from the party. In December, the party leadership formally presented the expulsion request to the Supreme Tribunal of the party, on the basis of his decision to ignore the party wishes on the Transantiago funding bill and for Zaldívar's harsh criticisms of the leadership's actions regarding corruption. The Tribunal finally decided to expel Zaldívar on December 27, 2007. On March 12, 2008 he became President of the Senate with the votes from the right-wing Alliance for Chile.
