It was first in all of the eastern German states except for Berlin and is poised for victory in upcoming elections in the states of Thuringia, Saxony and Brandeburg in September.
The party has been accused of racism for its hardline views on immigration, claims that its leaders deny.
On Saturday, protesters projected the anti-nazi slogan “never again” on the Grugahalle building, where the party was meeting, and attempted to block members from entering.
Several clashes broke out with police, who used tear gas to disperse the crowds. Two officers were hospitalised and 28 were injured.
The congress eventually happened, though half an hour later than scheduled due to the protests.
“We are here and we will stay,” said the AfD co-president, Alice Weidel.
“We have the right, like all political parties, to hold a congress.”
The AfD ended its second day of conference early to watch Germany defeat Denmark in the Euro 2024 tournament, in a match that was temporarily suspended due to heavy rain.