Groups of protesters blocked or tried to block roads in and around the city on Saturday morning.
Police said they used pepper spray after stones were thrown at officers at one location.
In another case, police said they used water cannons to clear a blockade by some 2000 protesters after they ignored calls to leave.
Previous youth organisation was dissolved in March
The new youth organisation of the anti-immigration Alternative for Germany, or AfD, is to be set up in a meeting at Giessen's convention center, which had yet to start two hours after the planned time.
Its predecessor, the Young Alternative - a largely autonomous group with relatively loose links to the party - was dissolved at the end of March after AfD decided to formally cut ties with it.
AfD wants to have closer oversight over the new group, expected to be called Generation Germany.
The party finished second in Germany's national election in February with more than 20 per cent of the vote and is now the country's biggest opposition party.
It has continued to rise in polls as Chancellor Friedrich Merz's coalition government has failed to impress voters.
Germany's domestic intelligence agency had concluded that the Young Alternative was a proven right-wing extremist group.
It later classified AfD itself as such a group, but suspended the designation after AfD launched a legal challenge.
In a ruling in 2024 rejecting a call for an injunction against the Young Alternative designation, a Cologne court argued that preserving an ethnically defined German people and the exclusion if possible of the "ethnically foreign" was a central political idea of the group.
It also pointed to agitation against migrants and asylum-seekers, and links with extremist groups such as the Identitarian Movement.
In June, a higher court ended the appeal process, noting the Young Alternative had been dissolved.
It's typical for German parties to have youth wings, which are generally more politically radical than the parties themselves.
It remains to be seen whether the new AfD youth organisation will be more moderate than its predecessor, with at least some continuity expected.
