Some threw garbage cans at Catalan police in riot gear, who responded by beating demonstrators with their batons or firing warning shots in the air.
"This Europe is shameful!," they chanted as they marched by the office of the European Commission in the Catalan capital.
Despite the efforts of Puigdemont, who fled to Brussels after the Catalan parliament declared independence on October 27th and Madrid countered by taking control of the region, no European Union member state backed the secessionist cause.
Outside of the German consulate demonstrators held up a photo of German Chancellor Angela Merkel sporting a Hitler-style moustache.
Many chanted "no more smiles", a reference to the longstanding claim from Catalan separatist leaders that their drive to break the wealthy northeastern region away from Spain would be a "revolution of smiles".
But other separatist leaders like Elsa Artadi, a lawmaker in the Catalan parliament for Puigdemont's Together for Catalonia party, appealed for calm.
The protest was called by the radical Committees for the Defence of the Republic (CDR), which were set up just before Catalonia held a referendum on independence on October 1 that was banned by the courts.
"They are not going to stop anything with these arrests, on the contrary," said Yolanda Salleras, a 37-year-old physiotherapist.
"They want to bury us but each time they hit us, four new separatists arise. They want to decapitate us but we are two million," she added.
Salleras said the time had come for separatists to do more than just hit the streets in protest.
Bins were set on fire during the protests. Photo: AFP
"We need something more radical. I would paralyse the country, a general strike lasting several days until they free everyone," she said.
According to Catalan public radio, CDR members blocked several roads in Catalonia, causing traffic jams, just as they did during two strikes in the region last year called to protest police violence during the independence referendum.
Catalonia's emergency services said 100 people had been treated for injuries during the clashes, including seven police officers. All injuries were minor.
Actualització dades 01h: el #SEM ha realitzat en total 100 atencions sanitàries per les mobilitzacions d’avui, principalment per contusions: 92 a Barcelona, totes de caràcter lleu (23 d’ells Mossos d’Esquadra) i 1 de menys greu i, per altra banda, 7 a Lleida i 1 a Tarragona lleus— SEM. Generalitat (@semgencat) March 25, 2018
Aside from Puigdemont, who was arrested in Germany on a European warrant issued by Spain, nine other Catalan separatist leaders are in jail over their role in the region's independence push.
Five other Catalan separatist leaders went into exile along with Puigdemont, who will now have to appear before a German judge who will decide if he is sent back to Spain to face trial.
"I hope they will not extradite him but I am not very optimistic," said Rosa Vela, a 60-year-old teacher.
Sirens wailed in the background throughout the protest which was held under an overcast sky.
Judit Carapena, a 22-year-old architecture student, said Spain's central government should not "sing victory because it is not the end of separatism, far from it."
"It's the people who fuel separatism and they can't put us all in jail. There will be other Puigdemonts," she added.
Polls show Catalans are almost evenly divided on the issue of independence but the vast majority back holding a legal referendum to settle the question.
"We are going to continue to resist and fight to be free," said Julio Vallmitjana, a bearded 64-year-old pensioner who wore his white hair in a pony tail and stood a bit apart from the crowd.
"Before I was in favour of confrontation but I realised that is not the best path. We have nothing more to do than to do things peacefully. The problem is that the good guys never win but we will be the first to do it."
By Daniel Bosque / AFP