Spain dissolved the regional government deposing Mr Puigdemont who could now be in prison within months.
It was revealed on Friday that Spanish prosecutors would charge Mr Puigdemont with rebellion, a crime which carries a possible sentence of 30 years.
Elections will be held in Catalonia on December 21 following the move to dissolve the government.
Questions have been raised about Mr Puigdemont’s eligibility for re-election following reports that he could face criminal charges.
Spain’s foreign minister, Alfonso Dastis, claimed the president could “theoretically” make a bid for re-election if he remains free until the vote.
Mr Dastis said: “I don’t know what kind of judicial activity will happen between now and 21 December.
“If he is not put in jail at that time I think he is not ineligible.”
The warning came as hundreds of thousands of protesters came out to support a united Spain in the highly divided region.
Demonstrators called for the Catalan leader to be locked up and chanted “Viva Espana” (long live Spain) and “Visca Catalunya” (long live Catalonia) in Barcelona.
The demonstrations came 48 hours after MPs in the region voted narrowly to declare independence with 70 out of 135 supporting the unilateral.
Some 1,700 firms loved their legal headquarters out of the region amid fears about the effects independence could have on business.
Catalonia overwhelming voted for independence in a referendum declared illegal by Spain’s central government.
Turnout was very low amid a boycott and a violent police crackdown with only 43 per cent making it to the polls.
Some polls have shown waining support for independence with anti-independence parties expected to win 43.4 per cent of the vote in December and pro-independence parties projected to win 42.5 per cent.
Mr Datis suggested Catalonia could win some new powers but rejected independence.
He said: “I rule out full independence but not necessarily more autonomy, even if they are now already one of the regions with the highest powers and competences not only in Spain but in the world at large.”