Clashes erupted as protesters took to the streets in Catalonia on Sunday following his arrest.
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.
Away from the extradition proceedings, the Catalan parliament has still not managed to form a new government in the wake of December's election, meaning Madrid continues to exert the direct rule it introduced in the region in October.
Former Catalan education minister Clara Ponsati will fight an worldwide order for her extradition to Spain from Scotland, arguing that as a secessionist leader she is not guaranteed a fair trial, her lawyer said on Monday.
German highway police stopped Puigdemont on Sunday morning near the A7 highway that leads into Germany from Denmark, police in the northern state of Schleswig-Holstein said.
Catalonia's police say nine people linked to the riots were arrested, five of whom have been released. "He has not been arrested".
Puigdemont and other exiled Catalan leaders have travelled to other countries in Europe despite efforts by Spain to seek their extradition.
A Spanish court reactivated on Friday a European arrest warrant against Puigdemont on charges of sedition and rebellion. Spain has also issued five warrants for other separatist who fled the country. Two more were hurt in a smaller clash in the town of Lleida.
"Indeed it is a political question and you should not make use of an European Arrest Warrant and force a, sort of, your fellow member states to cooperate with regards to this political discussion that you have ongoing in a state as a purely interior matter", said legal analyst Christoph Safferling.
Catalan Parliamentary President Roger Torrent pledged to defy the central government in Madrid.
The Spanish Supreme Court on Friday issued fresh arrest warrants against Puigdemont and six other Catalan politicians who now are overseas. Llarena ruled that a total of 25 Catalan separatists would be tried for rebellion, embezzlement or disobedience. The independence movement has been obsessed in recent months with gaining the support of the worldwide community and, in particular, the European Union.
Another election could swing the government either way, with separatist sympathies still simmering across Catalonia, though polls have shown support sharply down in recent months.