As president of the HDZ BiH, he took part in many constitutional reform talks, most notably in those regarding the Prud Agreement between 2008 and 2009, and in the 2010–2012 government formation.

In November 2006, Čović was sentenced to five years in prison for exempting the Ivanković-Lijanović company of paying taxes on meat imports.

In 2007, he became visiting professor at the University of Mostar's Faculty of Philosophy, and in 2014 member of the Croatian Academy of Sciences and Arts of Bosnia and Herzegovina.

[1] From 10 January 2001 to 12 March 2001, he served as Acting Prime Minister of the Federation of Bosnia and Herzegovina, succeeding the Party of Democratic Action's Edhem Bičakčić.

Čović served as Acting Prime Minister for two months, before he himself was succeeded by Alija Behmen of the Social Democratic Party.

[1] He served as Presidency member until 29 March 2005, when he was removed from office by the High Representative for Bosnia and Herzegovina, Paddy Ashdown, for abuse of power and position.

[citation needed] Together with the leaders of the three most important 'nationalist' political parties in Bosnia and Herzegovina, who acted as representatives of the constituent peoples, Milorad Dodik of the Alliance of Independent Social Democrats (SNSD) and Sulejman Tihić of the Party of Democratic Action, Čović created the Prud Agreement or Prud Process, an agreement that pertained to state property, census, constitutional changes, reconstructing the Council of Ministers of Bosnia and Herzegovina and solving the legal status of Brčko District.

[5] At a subsequent meeting in Banja Luka on 26 January 2009, the party leaders set out a plan for Bosnia and Herzegovina as a decentralized country with three levels of government.

[6] On 20 July 2009, the High Representative for Bosnia and Herzegovina, Valentin Inzko suggested that the process between the three 'nationalist' parties had effectively ended.

Following the 2010 general election, a process of formation of Bosnia and Herzegovina's Council of Ministers (i.e. the national government) began.

The European Union and the Office of the High Representative repeatedly attempted negotiations to appease the Bosniak–Bosnian and Serb–Croat divided political blocs, in parallel to the Bosnian constitutional crisis, all ending in failure.

The Bosniak-Bosnian coalition insisted that the seat would have to go to them as the party that received the largest number of votes, while the Serb–Croat alliance insisted that due to the fact that according to tradition, the next Chairman of the Council of Ministers must be an ethnic Croat, it must come from an authentic Croat party (Croatian Democratic Union), and not the multi-ethnic SDP BiH.

A round of talks between party leaders was held in Mostar on 5 September 2011, hosted by Croat politicians Božo Ljubić and Čović, with Milorad Dodik, Mladen Bosić, Sulejman Tihić and Zlatko Lagumdžija in attendance.

On the same day, an EU spokesperson warned that the country risked losing funding through the Instrument for Pre-Accession Assistance if the political situation did not stabilize.

[14][15] As “credible efforts” towards the implementation of the Sejdić–Finci ruling remained the outstanding condition for the entry into force of the Stabilisation and Association Agreement, in June 2012, Czech Commissioner Štefan Füle launched a High Level Dialogue on the Accession Process (HLAD) with Bosnia and Herzegovina, tackling both the Sejdić–Finci issue and the need for a coordination mechanism for the country to speak with a single voice in the accession process.

[16] In February 2013, the European Commission decided to step up its involvement, with the direct facilitation of talks by Füle, in coordination with the Council of Europe's Secretary-General Thorbjørn Jagland.

[17] In March and April 2013, with the support of the Director-General for Enlargement Stefano Sannino, the EU Delegation in Sarajevo facilitated a series of direct talks between party leaders, with no concrete outcome.

[18][16] During the summer of 2013, Čović and Bosnian Presidency member Bakir Izetbegović reached a political agreement on several files, from Mostar to Sejdić–Finci, in parallel to the initiative led by the U.S. Embassy for a constitutional reform of the Federal entity.

[16] Three further rounds of negotiations among political leaders were led together with Štefan Füle, in a castle near Prague in November 2013, and later in Sarajevo in the first months of 2014, also with the presence of the U.S. and the Venice Commission.

[1] He chaired the Presidency between November 2015 and March 2016, during which period on 15 February 2016, Bosnia and Herzegovina submitted its EU membership application.

In November 2006, Čović was sentenced to five years in prison for exempting the Ivanković-Lijanović company from paying taxes on meat imports.