More than 500 people gathered to hear Wilders speak at the Hotel Berlin. Meanwhile, a spokesman for Berlin's police said over 100 people gathered for a protest against the anti-Islam politician's visit.
The demonstration, which was organised by the Social Democrats and an association opposed to extreme-right politics, passed off peacefully.
Protestors, outnumbered by around 250 police, brandished photos of the shock-blond Wilders that portrayed him with a moustache similar to that worn by Adolf Hitler.
In his speech at the Hotel Berlin, Wilders claimed Germany's national identity, democracy and prosperity were threatened by Islamic political ideology. "A Germany full of mosques and full of veiled women is no longer the Germany of Schiller and Heine, Bach and Mendelssohn," he said.
The 47-year-old politician also took aim at Chancellor Merkel and Germany's established parties, accusing them of accepting the "Islamisation" of Germany.
Wilders was invited to speak in Berlin by ousted former conservative politician René Stadtkewitz, who recently announced he was forming a new "Freedom" party in Germany.
In an interview with the Sonntag Aktuell newspaper, Green party parliamentary group leader Jürgen Trittin said Wilders' visit was an "affront to Berlin's cosmopolitan tradition," in a city that is home to hundreds of thousands of Muslims. "We must stop all attempts by smug right-wing populists and Islamophobic bigots to marginalise and vilify these fellow citizens," he said.
Wilders' anti-immigration Freedom Party (PVV) won record support in the June election in the Netherlands, giving it the third highest vote and an unprecedented bargaining position.
At a special party congress in the Dutch city of Arnhem on Saturday, members of the Dutch Christian Democrats (CDA) agreed to a power deal with the Liberal party (VVD), which would rely on support from Wilders' PVV.
In the run-up to the decision, German politicians expressed concern over the pact.
Wilders is due to stand trial in Amsterdam on Monday on five charges of giving religious offence to Muslims and inciting hatred and discrimination against Muslims and people of non-western immigrant origin, particularly Moroccans.
The target of death threats, Wilders enjoys 24-hour state-sponsored protection while pursuing his mission to "stop the Islamisation of the Netherlands."