Shortly before 7am, "Many violent, masked, left-wing extremists attempted to gain entry to the exhibition center," and prevent the conference from taking place, a police spokesman told SWR Fernsehen.
The protestors also attempted to block access to the exhibition center's multi-storey car park.
Some of the protestors were armed with iron bars and planks of wood, and some attacked police with Bengal lights (a kind of firework), and flares.
Around 1,000 police officers had been stationed around the conference since dawn, equipped with water cannon. Eyewitnesses told SWR Fernsehen that the police used pepper spray to subdue some of the protestors.
The start of the AfD conference, at which the party is set to define its party manifesto ahead of Germany's federal elections next year, was delayed by one hour as a result of the protests.