In January 2016, following an agreement between the Junts pel Sí (JxSí), an electoral alliance of which ERC was a part, and the Popular Unity Candidacy (CUP), Junqueras was appointed Vice President of Catalonia.

[8][9][10] On the other hand, many voters who did not support Catalan independence did not turn out,[11] as the constitutional political parties asked citizens not to participate in what they considered an illegal referendum.

On 30 October 2017, charges of rebellion, sedition, and misuse of public funds were brought against Junqueras and other members of the Puigdemont government.

[15] The European Court of Justice ruled on 19 December 2019 that Junqueras had parliamentary immunity as he was an elected MEP, and should have been released from prison.

[27] JuntsxSVH formed an administration with the Convergence and Union (CiU) and the Initiative for Catalonia Greens-United and Alternative Left (ICV-EUiA-E) and Junqueras became Mayor of Sant Vicenç dels Horts.

[36][37] Despite the agreement, and protests form the Socialists and Greens, Junqueras was appointed Leader of the Opposition in the Catalan Parliament in January 2013.

[39] In January 2016, following a last-minute agreement between pro-Catalan independence parties JxSí and Popular Unity Candidacy (CUP) to replace Mas, Junqueras was appointed Vice President of Catalonia and Minister of Economy and Finance.

[44][45] The Catalan Parliament passed legislation on 6 September 2017 authorising the referendum which would be binding and based on a simple majority without a minimum threshold.

[59][60] Almost immediately the Senate of Spain invoked article 155 of the constitution, dismissing Puigdemont and the Catalan government and imposing direct rule on Catalonia.

[61][62] The following day Spanish Prime Minister Mariano Rajoy dissolved the Catalan Parliament and called for fresh regional elections on 21 December 2017.

[63][64] On 30 October 2017 Spanish Attorney General José Manuel Maza laid charges of rebellion, sedition and misuse of public funds at the Audiencia Nacional against Puigdemont, Junqueras and other members of the Catalan government.

[67] On 2 November 2017 Audiencia Nacional judge Carmen Lamela remanded in custody Junqueras and seven other Catalan ministers (Dolors Bassa, Meritxell Borràs, Joaquim Forn, Carles Mundó, Raül Romeva, Josep Rull and Jordi Turull) as she considered them a flight risk.

[74][75] They were allegedly handcuffed behind their backs without seat belts in a van going very fast, forced to listen to the Spanish national anthem on a loop and threatened by their guards.

[75][76][77] Earlier, as the ministers arrived at the Audiencia Nacional, Spanish police officers were shown, in video obtained Reuters and published by the La Vanguardia, making sneering, homophobic comments about the ministers, with one officer saying "Wait till you see what they do to the little teddy bear", referring to Junqueras, "When they get him on all fours, they’ll fix his eye".

[82][83][84] On 4 December 2017 Llarena released, after 32 days in prison, six of the ministers (Bassa, Borrás, Mundó, Romeva, Rull and Turull) on bail of €100,000 but ordered that their passports be confiscated.

[87][88][89] In denying them bail, Llarena claimed that it remained to be seen if their pledge to abide by Spanish law was "truthful and real" and that there was a risk that they would commit the same crimes if released.

[94][95] Junqueras was denied bail on 5 January 2018 by Supreme Court judges Miguel Colmenero, Alberto Jorge Barreiro and Francisco Monterde who said that "there is no sign that the defendant has any intention of abandoning the route he has followed until now".

[109][110] The European Court of Justice ruled on 19 December 2019 that Junqueras had parliamentary immunity as he was an elected MEP and should have been released from prison.

[16] On 22 June 2021, the Government of Spain formally pardoned Junqueras and eight other Catalan politicians for their roles in the unilateral declaration of independence.