German police arrested Puigdemont on Sunday, after he crossed the border from Denmark, under a European warrant issued by Spain.
The arrest comes five months after Puigdemont went on the run as Spanish prosecutors sought to charge him with sedition and rebellion in the wake of a vote by the Catalan parliament to declare independence.
According to his lawyer Jaume Alonso-Cuevillas, he was on his way to Belgium, where he fled after Spanish authorities moved to impose direct rule over Catalonia.
Puigdemont will be brought before a German judge Monday to confirm his identity and a court will then decide if he is to remain in custody pending extradition proceedings.
"It will take place in the course of the day, probably in the afternoon," a spokeswoman for the prosecutor's office for Schleswig-Holstein state told AFP.
Calling the situation "very delicate", Alonso-Cuevillas told Catalonia's Rac1 radio it was "very likely that he will not be allowed to leave Germany".
Clashes erupted as protesters took to the streets in Catalonia on Sunday following his arrest.
Catalan police decked out in riot gear shoved and hit demonstrators with batons to keep the crowd from advancing on the office of the Spanish government's representative in Barcelona, the capital of the wealthy northeastern region.
Officers fired warning shots in the air to try to contain the demonstrators, who pushed large recycling containers towards police. Some people threw glass bottles, cans and eggs at police.
Some 90 people were slightly injured during the protests in Barcelona, including 22 police officers, emergency services said.
Another seven people were injured at a protest in Lleida, about 150 kilometres west of Barcelona and one person was injured in Tarragona to the south.
It is the latest chapter in a secession saga that has bitterly divided Catalans and triggered Spain's worst political crisis in decades.
'Not the end'
"It angers us that they arrested Puigdemont, he is our highest representative," 22-year-old architecture student Judit Carapena told AFP at the protest.
Spain's central government should not "sing victory because it is not the end of separatism, far from it", she added.
Catalan parliament speaker Roger Torrent appealed for calm in an address broadcast on regional television.
"I have no doubt that Catalan society will act as it always has, with non-violence," he said.
Aside from Puigdemont, nine other Catalan separatist leaders are in jail in Spain over the region's failed bid for independence.
His arrest comes two days after Spain's supreme court issued international arrest warrants for 13 Catalan separatists including Puigdemont and his nominated successor Jordi Turull.
The court said they would be prosecuted for "rebellion", a charge which carries a maximum sentence of 30 years in prison.
Twelve more face less serious charges like disobedience.
Issuing the warrant for Puigdemont on Friday, Judge Pablo Llarena accused the ousted Catalan leader of organising an independence referendum in October last year despite a ban from Madrid.
The vote had been swiftly followed by the Catalan parliament's declaration of independence on October 27th.
As Spanish authorities moved in to impose direct rule over the region, Puigdemont and four other separatist leaders fled to Belgium. A sixth one fled the country on Friday, reportedly to Switzerland.
Hours after Puigdemont was detained in Germany, a spokesman from Police Scotland said one of them, Clara Ponsati, who has since gone to Scotland and is wanted for both rebellion and misuse of public funds, was "making arrangements" to surrender to authorities there.
Puigdemont had been visiting Finland since Thursday, but slipped out of the Nordic country before Finnish police could detain him.
Elsa Artadi, a lawmaker with Puigdemont's Together for Catalonia party, said that he should fight his extradition.
"Spain does not guarantee a fair trial; only revenge and repression," she wrote on Twitter.
"What they are doing these days is totally disproportionate, we are being treated like criminals for wanting independence," Rosa Vela, a 60-year-old teacher, told AFP at the protest in Barcelona.
While separatist parties won Catalonia's regional elections in December called by Madrid, they have been unable to elect a president and form a government as they have picked candidates are now either in exile, in jail or facing prosecution.
After Puigdemont was forced to withdraw his bid for the presidency as he could not return to Spain without facing arrest, another pro-independence leader Jordi Sanchez followed suit when a judge refused to let him out of jail to be sworn in. The third candidate, Turull, was placed in custody on Friday.
Fresh regional elections will be triggered if a new leader is not elected by May 22nd.