Mr Puigdemont and former cabinet members Toni Comin and Clara Ponsati left Spain following their organisation of a 2017 independence referendum that was subsequently ruled illegal by Spain’s Constitutional Court.
The vote triggered a political crisis in the country and led to Mr Puigdemont and Mr Comin taking self-imposed exile in Belgium, while Ms Ponsati is currently in Scotland.
Mr Puigdemont and Mr Comin became members of the European parliament in June 2019 and Ms Ponsati has been an MEP since February 2020.
The decision made by EU lawmakers on Tuesday to strip the trio of immunity could assist their extradition to Spain, where they have been charged with sedition.
Spain’s foreign minister, Arancha Gonzalez Laya, said the decision was a sign of “respect for the work of the Spanish justice system” and that a European lawmaker cannot use the role to “protect himself from appearing in a national court”.
“Problems in Catalonia are solved in Spain, not in Europe,” she said, defending a solution through dialogue.
The European parliament said it was for national judicial systems of EU countries to determine criminal proceedings.
Belgium has so far denied Spain’s requests. In January, a court refused to extradite Lluis Puig, another separatist former member of the Catalan government living in Belgium, over charges of misuse of public funds.
Mr Puigdemont has also been charged with misuse of public funds.
“We will not give up,” his party, Junts per Catalunya, wrote on Twitter after the EU parliament’s announcement.
“The political conflict between Catalonia and Spain has stopped being an internal affair. We have brought it to the heart of Europe to continue denouncing the repression and political persecution of the Spanish state,” it said.
Various independence leaders were convicted in Spain of the same charge of sedition in 2019 and sentenced to up to 13 years in prison.
The European parliament’s legal affairs committee voted last month that immunity from prosecution should be waived. In each case, the vote was 15 in favour, eight against and two abstentions.
Additional reporting from Reuters